Container for the list of vertices and the edges that connect them. More...

Inheritance diagram for denoptim.graph.DGraph:

Collaboration diagram for denoptim.graph.DGraph:

Classes
class	DENOPTIMGraphDeserializer

class	DENOPTIMGraphSerializer
	We expect unique IDs for vertices. More...

class	EdgeFinder
	Utility to make selection of edges to a vertex tunable by a parameter. More...

enum	StringFormat
	Identifier for the format of string representations of a graph. More...

Public Member Functions
	DGraph (List< Vertex > gVertices, List< Edge > gEdges)

	DGraph (List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings)

	DGraph (List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings, List< SymmetricVertexes > symSets)

	DGraph (List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings, List< ClosableChain > closableChains, List< SymmetricVertexes > symVertices)

	DGraph ()

void	setCandidateOwner (Candidate candidate)
	Sets the reference to the candidate item that is defined by this graph. More...

Candidate	getCandidateOwner ()
	Returns the reference of the candidate item that is defined by this graph. More...

void	setGraphId (int id)

int	getGraphId ()

void	setLocalMsg (String msg)

String	getLocalMsg ()

boolean	hasSymmetricAP ()

boolean	hasSymmetryInvolvingVertex (Vertex v)

int	getSymmetricSetCount ()
	Returns the number of symmetric sets of vertices. More...

Iterator< SymmetricVertexes >	getSymSetsIterator ()
	Get an iterator for the sets of symmetrically related vertices. More...

List< Vertex >	getSymVerticesForVertex (Vertex v)

boolean	detectSymVertexSets () throws DENOPTIMException
	Tries to determine the set of symmetric vertices in this graph based on finding compatible `Vertex`es that are either using symmetric `AttachmentPoint`s (NB: all symmetric APs must be in use by vertexes that are compatible with each other) or that are downstream (i.e., according to edge direction) w.r.t `Vertex`es that are using symmetric `AttachmentPoint`s.The compatibility of the vertexes is determined by these criteria: More...

void	removeSymmetrySet (SymmetricVertexes ss)
	Removed the given symmetric set, if present. More...

SymmetricVertexes	getSymSetForVertex (Vertex v)
	Returns the set of vertexes symmetric to the given one. More...

void	setSymmetricVertexSets (List< SymmetricVertexes > symVertices)

void	addSymmetricSetOfVertices (SymmetricVertexes symSet) throws DENOPTIMException
	Adds a symmetric set of vertices to this graph. More...

void	setVertexList (ArrayList< Vertex > vertices)

void	setEdgeList (ArrayList< Edge > edges)

void	setRings (ArrayList< Ring > rings)

void	setCandidateClosableChains (ArrayList< ClosableChain > closableChains)

List< ClosableChain >	getClosableChains ()

List< Vertex >	getVertexList ()

Vertex	getSourceVertex ()
	Identifies and return the vertex from which the spanning tree originates. More...

List< Edge >	getEdgeList ()

List< Ring >	getRings ()

List< Edge >	getEdgesWithSrc (Vertex v)
	Returns the list of edges that depart from the given vertex, i.e., edges where the srcAP is owned by the given vertex. More...

List< Edge >	getEdgesWithTrg (Vertex v)
	Returns the list of edges that arrive from the given vertex, i.e., edges where the trgAP is owned by the given vertex. More...

ArrayList< Ring >	getRingsInvolvingVertex (Vertex v)
	Returns the list of rings that include the given vertex in their fundamental cycle. More...

ArrayList< Ring >	getRingsInvolvingVertex (Vertex[] vs)
	Returns the list of rings that include the given list of vertices in their fundamental cycle. More...

ArrayList< Ring >	getRingsInvolvingVertexID (int vid)

boolean	hasRings ()
	Check for rings in this graph. More...

boolean	hasOrEmbedsRings ()
	Check for rings in this graph and in any graph that is embedded at any level in any vertex of this graph. More...

boolean	isVertexIDInRing (int vid)

boolean	isVertexInRing (Vertex v)

ArrayList< Vertex >	getRCVertices ()
	Search for ring closing vertices: vertices that contain only a `RingClosingAttractor` More...

ArrayList< Vertex >	getFreeRCVertices ()
	Search for unused ring closing vertices: vertices that contain only a `RingClosingAttractor` and are not part of any `DENOPTIMRing` More...

ArrayList< Vertex >	getUsedRCVertices ()
	Search for used ring closing vertices: vertices that contain only a `RingClosingAttractor` and are part of a `DENOPTIMRing`. More...

void	addEdge (Edge edge)
	Adds the edge to the list of edges belonging to this graph. More...

void	addRing (Ring ring)

void	addRing (Vertex vI, Vertex vJ) throws DENOPTIMException
	Adds a chord between the given vertices, thus adding a ring in this graph. More...

void	addRing (Vertex vI, Vertex vJ, BondType bndTyp)
	Adds a chord between the given vertices, thus adding a ring in this graph. More...

void	addVertex (Vertex vertex) throws DENOPTIMException
	Appends a vertex to this graph without creating any edge. More...

void	removeVertex (Vertex vertex)
	Remove a vertex from this graph. More...

boolean	removeVertexAndWeld (Vertex vertex, FragmentSpace fragSpace) throws DENOPTIMException
	Remove a given vertex belonging to this graph and re-connects the resulting graph branches as much as possible. More...

boolean	removeSingleVertexAndWeld (Vertex vertex, FragmentSpace fragSpace) throws DENOPTIMException
	Remove a given vertex belonging to this graph and re-connects the resulting graph branches as much as possible. More...

void	replaceUnusedRCVsWithCapps (FragmentSpace fragSpace) throws DENOPTIMException
	Removes unused ring-closing vertices. More...

boolean	replaceSubGraph (List< Vertex > subGrpVrtxs, DGraph incomingGraph, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap, FragmentSpace fragSpace) throws DENOPTIMException
	Replaced the subgraph represented by a given collection of vertices that belong to this graph. More...

List< List< Vertex > >	getSymmetricSubGraphs (List< Vertex > subGrpVrtxs) throws DENOPTIMException
	We assume that the subgraph is a continuously connected, directed graph. More...

boolean	replaceSingleSubGraph (List< Vertex > subGrpVrtxs, DGraph newSubGraph, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap) throws DENOPTIMException
	Replaced the subgraph represented by a given collection of vertices that belong to this graph. More...

boolean	replaceVertex (Vertex vertex, int bbId, BBType bbt, LinkedHashMap< Integer, Integer > apIdMap, FragmentSpace fragSpace) throws DENOPTIMException
	Replaced a given vertex belonging to this graph with a new vertex generated specifically for this purpose. More...

boolean	replaceVertex (Vertex vertex, int bbId, BBType bbt, LinkedHashMap< Integer, Integer > apIdMap, boolean symmetry, FragmentSpace fragSpace) throws DENOPTIMException
	Replaced a given vertex belonging to this graph with a new vertex generated specifically for this purpose. More...

boolean	insertVertex (Edge edge, int bbId, BBType bbt, LinkedHashMap< AttachmentPoint, Integer > apMap, FragmentSpace fragSpace) throws DENOPTIMException
	Inserts a given vertex in between two vertices connected by the given edge. More...

boolean	insertSingleVertex (Edge edge, Vertex newLink, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap) throws DENOPTIMException
	Inserts a given vertex in between two vertices connected by the given edge. More...

Vertex	getVertexAtPosition (int pos)
	Returns the vertex that is in the given position of the list of vertices belonging to this graph. More...

boolean	containsOrEmbedsVertex (Vertex v)
	Check if the specified vertex is contained in this graph as a node or in any inner graphs that may be embedded in `Template`-kind vertex belonging to this graph. More...

boolean	containsVertex (Vertex v)
	Check if this graph contains the specified vertex. More...

int	indexOf (Vertex v)
	Returns the index of a vertex in the list of vertices of this graph. More...

Vertex	getVertexWithId (long vid)
	Searches for a vertex with the given identifier. More...

int	indexOfVertexWithID (long vid)
	Returns the position of the first vertex that has the given ID. More...

void	removeEdge (Edge edge)
	Removes an edge and update the free valences of the attachment points that were originally involved in this edge. More...

void	removeRing (Ring ring)

Edge	getEdgeAtPosition (int pos)

int	getEdgeCount ()

int	getRingCount ()

int	getVertexCount ()

String	toString ()

int	getBondingAPIndex (Vertex srcVert, int dapidx, Vertex dstVert)

ArrayList< Vertex >	getChildVertices (Vertex vertex)

void	getChildrenTree (Vertex vertex, List< Vertex > children)
	Gets all the children of the current vertex recursively. More...

void	getChildrenTree (Vertex vertex, List< Vertex > children, boolean markBranches)
	Gets all the children of the current vertex recursively. More...

void	getChildrenTree (Vertex vertex, List< Vertex > children, AtomicInteger branchIdGenerator, List< Integer > prevBranchId)
	Gets all the children of the current vertex recursively. More...

void	getChildrenTree (Vertex vertex, List< Vertex > children, int numLayers, boolean stopBeforeRCVs)
	Gets all the children of the current vertex recursively. More...

List< Integer >	getBranchIdOfVertexAtPosition (int i)
	Returns the branch identifier. More...

List< Integer >	getBranchIdOfVertex (Vertex v)
	Returns the branch identifier. More...

String	getBranchIdOfVertexAsStr (Vertex v)
	Returns the branch identifier as a literal string. More...

boolean	directedPathExists (Vertex src, Vertex trg)
	Uses branch identifiers to define is two vertices are in such a relation that allows the drawing of a directed path from one to the other. More...

void	getChildTreeLimited (Vertex vertex, List< Vertex > children, boolean stopBeforeRCVs)
	Gets all the children of the current vertex recursively. More...

void	getChildTreeLimited (Vertex vertex, List< Vertex > children, Set< Vertex > limits)
	Gets all the children of the current vertex recursively until it finds one of the vertices listed as limit. More...

void	getChildTreeLimited (Vertex vertex, List< Vertex > children, List< Vertex > limitsInClone, boolean stopBeforeRCVs)
	Gets all the children of the current vertex recursively until it finds one of the vertices listed as limit. More...

Vertex	getDeepestAmongThese (List< Vertex > list)
	Identify the oldest ancestor (i.e., most great grandparent) in the given collection. More...

void	getParentTree (Vertex vertex, List< Vertex > parentTree)
	Traverse the graph until it identifies the source of the directed path reachable from the given vertex recursively. More...

Vertex	getParent (Vertex v)

DGraph	clone ()
	Returns almost "deep-copy" of this graph. More...

Edge	getEdgeWithParent (long l)
	Looks for an edge that points to a vertex with the given vertex id. More...

ArrayList< Integer >	getIndexOfEdgesWithChild (int vid)

ArrayList< Edge >	getEdgesWithChild (int vid)

long	getMaxVertexId ()

boolean	containsVertexID (long l)
	Checks if a number is already used as VertexIDs within the graph. More...

void	cleanup ()
	Wipes the data in this graph. More...

boolean	isIsomorphicTo (DGraph other)
	Checks if this graph is "DENOPTIM-isomorphic" to the other one given. More...

boolean	isIsostructuralTo (DGraph other)
	Checks if this graph is "DENOPTIM-isostructural" to the other one given. More...

boolean	sameAs (DGraph other, StringBuilder reason)
	Compare this and another graph ignoring the vertex IDs. More...

boolean	containsAtoms ()
	Returns `true` if this graph has any vertex that contains atoms. More...

int	getHeavyAtomsCount ()
	Calculate the number of atoms from the graph representation. More...

ArrayList< AttachmentPoint >	getAttachmentPoints ()
	Returns the list of all attachment points contained in this graph. More...

ArrayList< AttachmentPoint >	getAvailableAPs ()
	Returns the list of available attachment points contained in this graph. More...

List< AttachmentPoint >	getAvailableAPsThroughout ()
	Returns the list of attachment points contained in this graph that are available throughout the template barrier, i.e., are free in this graph an in any embedding graph that containing this one. More...

AttachmentPoint	getAPWithId (int id)
	Returns the attachment point with the given identifier, or null if no AP is found with the given identifier. More...

boolean	graphNeedsCappingGroups (FragmentSpace fragSpace)
	Checks the graph for unused APs that need to be capped. More...

void	removeCappingGroupsOn (Vertex vertex)
	Remove capping groups on the given vertex of this graph. More...

void	removeCappingGroups (List< Vertex > lstVerts)
	Remove capping groups that belong to this graph and are in the given list. More...

void	removeCappingGroupsFromChilds (List< Vertex > lstVerts)

void	removeCappingGroups ()
	Remove all capping groups on this graph. More...

void	addCappingGroups (FragmentSpace fragSpace) throws DENOPTIMException
	Add a capping groups on free unused attachment points. More...

void	addCappingGroups (List< Vertex > vertexAddedToThis, FragmentSpace fragSpace) throws DENOPTIMException
	Add a capping group on the given vertices, if needed. More...

DGraph	extractSubgraph (int index) throws DENOPTIMException
	Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex. More...

DGraph	extractSubgraph (Vertex seed) throws DENOPTIMException
	Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex. More...

DGraph	extractSubgraph (Vertex seed, int numLayers, boolean stopBeforeRCVs) throws DENOPTIMException
	Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex and visiting at most a given number of vertex layers, and optionally stopping the exploration of a branch before including any ring-closing vertex. More...

DGraph	extractSubgraph (Vertex seed, List< Vertex > limits, boolean stopBeforeRCVs) throws DENOPTIMException
	Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex and stopping the exploration at the given end vertices (i.e., limits). More...

DGraph	extractSubgraph (Vertex seed, boolean stopBeforeRCVs) throws DENOPTIMException
	Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex. More...

List< DGraph >	extractPattern (GraphPattern pattern) throws DENOPTIMException
	Extracts subgraphs that match the provided pattern. More...

Map< DGraph, ObjectPair >	extractPattern (GraphPattern pattern, boolean recordConnectivity) throws DENOPTIMException
	Extracts subgraphs that match the provided pattern. More...

DGraph	extractSubgraph (Collection< Vertex > definedOn)
	Returns a clone of the subgraph defined by the a collection of vertices belonging to this graph. More...

DGraph	extractSubgraph (Collection< Vertex > definedOn, Set< Edge > connectionToSubgraph, Set< Edge > connectionFromSubgraph)
	Returns a clone of the subgraph defined by the a collection of vertices belonging to this graph. More...

DGraph	embedPatternsInTemplates (GraphPattern pattern, FragmentSpace fragSpace) throws DENOPTIMException
	Searches for the given pattern type and generated a new graph where each set of (clones of) vertexes that define one such patterns is embedded in a single template. More...

DGraph	embedPatternsInTemplates (GraphPattern pattern, FragmentSpace fragSpace, ContractLevel contract) throws DENOPTIMException
	Searches for the given pattern type and generated a new graph where each set of (clones of) vertexes that define one such patterns is embedded in a single template. More...

boolean	removeBranchStartingAt (Vertex v, boolean symmetry) throws DENOPTIMException
	Deletes the branch, i.e., the specified vertex and its children. More...

boolean	removeBranchStartingAt (Vertex v) throws DENOPTIMException
	Deletes the branch, i.e., the specified vertex and its children. More...

boolean	removeOrphanBranchStartingAt (Vertex v) throws DENOPTIMException
	Deletes the branch, i.e., the specified vertex and its children. More...

boolean	removeChainUpToBranching (Vertex v, FragmentSpace fragSpace) throws DENOPTIMException
	Mutates the graph by removing the chain where a given vertex is located up to the first branching (i.e., to non-capping group) on either side. More...

void	changeSignOfVertexID ()
	Change all vertex IDs to the corresponding negative value. More...

void	renumberGraphVertices ()
	Reassign vertex IDs to all vertices of this graph. More...

Map< Long, Long >	renumberVerticesGetMap ()
	Reassign vertex IDs to a graph. More...

int	getLevel (Vertex v)
	Calculates the level of a vertex in this graph. More...

Object[]	checkConsistency (RunTimeParameters settings) throws DENOPTIMException
	Peeks into this graph to derive a preliminary chemical representation with SMILES and InChIKey. More...

Object[]	checkConsistency (RunTimeParameters settings, boolean permissive) throws DENOPTIMException
	Peeks into this graph to derive a preliminary chemical representation with SMILES and InChIKey. More...

ArrayList< DGraph >	makeAllGraphsWithDifferentRingSets (RunTimeParameters settings) throws DENOPTIMException
	Evaluates the possibility of closing rings in this graph and generates all alternative graphs resulting by different combinations of rings. More...

boolean	hasForbiddenEnd (FragmentSpaceParameters fsSettings)
	Check if there are forbidden ends: free attachment points that are not suitable for capping and not allowed to stay unused. More...

void	appendGraphOnGraph (List< Vertex > parentVertices, List< Integer > parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, boolean onAllSymmAPs) throws DENOPTIMException
	Append a graph (incoming=I) onto this (receiving=R). More...

void	appendVertexOnAP (AttachmentPoint srcAP, AttachmentPoint trgAP) throws DENOPTIMException
	Append a vertex to this graph: adds the new vertex to the list of vertices belonging to the graph, and adds the resulting edge to the graph. More...

void	appendGraphOnAP (AttachmentPoint apOnThisGraph, AttachmentPoint apOnIncomingGraph, BondType bndType) throws DENOPTIMException
	Appends a graph onto this graph. More...

void	appendGraphOnAP (Vertex parentVertex, int parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, Map< Vertex, SymmetricVertexes > newSymSets) throws DENOPTIMException
	Append a subgraph (I) to this graph (R) specifying which vertex and attachment point to use for the connection. More...

void	appendGraphOnGraph (Vertex parentVertex, int parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, Map< Vertex, SymmetricVertexes > newSymSets, boolean onAllSymmAPs) throws DENOPTIMException
	Append a graph (incoming=I) onto this graph (receiving=R). More...

List< Long >	findVerticesIds (VertexQuery query, Logger logger)
	Search a graph for vertices that match the criteria defined in a query vertex. More...

ArrayList< Vertex >	findVertices (VertexQuery vrtxQuery, Logger logger)
	Filters a list of vertices according to a query. More...

ArrayList< Vertex >	findVertices (VertexQuery vrtxQuery, boolean purgeSym, Logger logger)
	Filters a list of vertices according to a query. More...

void	removeSymmetryRedundance (List< Vertex > list)
	Remove all but one of the symmetry-related partners in a list of vertices. More...

void	removeSymmetryRedundantIds (ArrayList< Long > list)
	Remove all but one of the symmetry-related partners in a given list of vertex IDs. More...

DGraph	editGraph (ArrayList< GraphEdit > edits, boolean symmetry, FragmentSpace fragSpace, Logger logger) throws DENOPTIMException
	Edit this graph according to a given list of edit tasks. More...

List< Vertex >	getMutableSites ()
	A list of mutation sites from within this graph. More...

List< Vertex >	getMutableSites (List< MutationType > ignoredTypes)
	A list of mutation sites from within this graph. More...

String	toJson ()
	Produces a string that represents this graph and that adheres to the JSON format. More...

boolean	hasScaffoldTypeVertex ()
	Checks if this graph contains a scaffold vertex. More...

void	setTemplateJacket (Template template)
	Sets the reference to a template that embeds this graph, i.e., this graph's "jacket" template. More...

Template	getTemplateJacket ()

DGraph	getOutermostGraphOwner ()

List< Template >	getEmbeddingPath ()
	Find the path that one has to traverse to reach this graph from any template-embedding structure. More...

void	storeCurrentVertexIDs ()
	Copies the current vertexID of each vertex into a property of the vertex itself. More...

AttachmentPoint	getAPOnLeftVertexID (long nbrVid, long vid)
	Finds the AP that is on the first given parameter and that is used to make a connection to the second vertex, no matter the direction of the edge. More...

boolean	isReversible (FragmentSpace fragSpace)
	Checks is the every edge in the graph can be defined in the opposite direction according to the `APClass` compatibility rules. More...

List< AttachmentPoint >	getInterfaceAPs (List< Vertex > subGraphB)
	Searches for all `AttachmentPoint`s that represent the interface between a subgraph, identified by the given list of vertices, and any other vertex, i.e., either belonging to the same graph but not to the same subgraph, or belonging to an outer embedding level. More...

List< AttachmentPoint >	getSubgraphAPs (List< Vertex > subGraphB)
	Searches for all `AttachmentPoint`s that are owned by vertices in a subgraph but either available or used by vertices that do not belong to the subgraph. More...

Static Public Member Functions
static boolean	areApsUsedBySymmetricUsers (AttachmentPoint apA, AttachmentPoint apB, Set< Vertex > alreadyAssignedVrtxs)
	Checks if the `Vertex`s that are attached to two given `AttachmentPoint`s apA and apB satisfy these conditions: More...

static boolean	compareGraphNodes (Vertex thisV, DGraph thisG, Vertex otherV, DGraph otherG) throws DENOPTIMException
	Compares graphs by spanning vertices starting from the given vertex and following the direction of edges. More...

static DGraph	fromJson (String json)
	Reads a JSON string and returns an instance of this class. More...

static DGraph	fromJson (Reader reader)
	Reads a JSON string and returns an instance of this class. More...

static void	setScaffold (Vertex v)
	Update the graph so that the vertex argument is at the scaffold level i.e. More...

static DGraph	getEmbeddedGraphInClone (DGraph graphY, DGraph graphB, List< Template > path)
	Searches for a graphs (X) embedded at any level in a graph (Y) by knowing. More...

Protected Member Functions
void	reassignSymmetricLabels ()
	Marks the vertices of this graph with a string that is consistent for all vertices that belong to symmetric sets. More...

void	convertSymmetricLabelsToSymmetricSets ()
	Looks for any symmetric labels, creates symmetric sets that collect the same information, and removes the original symmetric labels. More...

int	getUniqueAPIndex ()

void	ensureUniqueApIDs ()

Package Functions
Map< SymmetricAPs, List< Vertex > >	findSymmetrySetsOfChildVertexes (Vertex vrtx, Set< Vertex > alreadyAssignedVrtxs)

Package Attributes
List< Vertex >	gVertices
	The vertices belonging to this graph. More...

List< Edge >	gEdges
	The edges belonging to this graph. More...

List< Ring >	gRings
	The rings defined in this graph. More...

List< ClosableChain >	closableChains
	The potentially closable chains of vertices. More...

int	graphId

String	localMsg
	A free-format string used to record simple properties in the graph. More...

Candidate	candidate
	Reference to the candidate entity owning this graph, or null. More...

Template	templateJacket
	Reference to the `Template` embedding this graph. More...

Private Member Functions
boolean	sameAsRings (StringBuilder reason, Map< Vertex, Vertex > vertexMap, Ring rT, Vertex vhT, Vertex vtT, Ring rO)

Static Private Member Functions
static boolean	compareGraphNodes (Vertex seedOnA, DGraph gA, Vertex seedOnB, DGraph gB, Map< Vertex, Vertex > vertexMap, StringBuilder reason) throws DENOPTIMException
	Compares graphs by spanning vertices starting from the given vertex and following the direction of edges. More...

static void	reorderVertexList (DGraph g)
	Sets the vertex at the lowest level as the scaffold, changes the directions of edges so that the scaffold is the source, and changes the levels of the graph's other vertices to be consistent with the new scaffold. More...

static void	fixEdgeDirections (DGraph graph)
	Flips edges in the graph so that the scaffold is the only source vertex. More...

static void	fixEdgeDirections (Vertex v, Set< Long > visited)
	Recursive utility method for fixEdgeDirections(graph). More...

Private Attributes
List< SymmetricVertexes >	symVertices

DefaultUndirectedGraph< Vertex, UndirectedEdge >	jGraph = null
	JGraph representation used to detect DENOPTIM-isomorphism. More...

DefaultUndirectedGraph< Node, NodeConnection >	jGraphKernel = null
	JGraph representation used to detect DENOPTIM-isostructural graphs. More...

AtomicInteger	apCounter = new AtomicInteger(1)
	Generator of unique AP identifiers within this graph. More...

Detailed Description

Container for the list of vertices and the edges that connect them.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 101 of file DGraph.java.

Constructor & Destructor Documentation

◆ DGraph() [1/5]

denoptim.graph.DGraph.DGraph	(	List< Vertex >	gVertices,
		List< Edge >	gEdges
	)

Definition at line 176 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.localMsg, and denoptim.graph.DGraph.symVertices.

◆ DGraph() [2/5]

denoptim.graph.DGraph.DGraph	(	List< Vertex >	gVertices,
		List< Edge >	gEdges,
		List< Ring >	gRings
	)

Definition at line 190 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.localMsg, and denoptim.graph.DGraph.symVertices.

◆ DGraph() [3/5]

denoptim.graph.DGraph.DGraph	(	List< Vertex >	gVertices,
		List< Edge >	gEdges,
		List< Ring >	gRings,
		List< SymmetricVertexes >	symSets
	)

Definition at line 201 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, and denoptim.graph.DGraph.localMsg.

◆ DGraph() [4/5]

denoptim.graph.DGraph.DGraph	(	List< Vertex >	gVertices,
		List< Edge >	gEdges,
		List< Ring >	gRings,
		List< ClosableChain >	closableChains,
		List< SymmetricVertexes >	symVertices
	)

Definition at line 212 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.localMsg, and denoptim.graph.DGraph.symVertices.

◆ DGraph() [5/5]

denoptim.graph.DGraph.DGraph ( )

Definition at line 223 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.localMsg, and denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.embedPatternsInTemplates(), and denoptim.graph.DGraph.replaceVertex().

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Member Function Documentation

◆ addCappingGroups() [1/2]

void denoptim.graph.DGraph.addCappingGroups ( FragmentSpace fragSpace ) throws DENOPTIMException

Add a capping groups on free unused attachment points.

Addition of Capping groups does not update the symmetry table for a symmetric graph.

Definition at line 4169 of file DGraph.java.

References denoptim.graph.DGraph.addCappingGroups(), and denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.addCappingGroups(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.buildGraph(), and denoptim.graph.DGraph.replaceSubGraph().

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◆ addCappingGroups() [2/2]

void denoptim.graph.DGraph.addCappingGroups	(	List< Vertex >	vertexAddedToThis,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Add a capping group on the given vertices, if needed.

The need for such groups is manifest when an attachment point that is not used in this or any embedding lever (i.e., attachment point is AttachmentPoint#isAvailableThroughout()) has and APClass that demands to be capped. Addition of Capping groups does not update the symmetry table for a symmetric graph.

Parameters

vertexAddedToThis list of vertices to operate on. They must belong to this graph.

Exceptions

DENOPTIMException if the addition of capping groups cannot be performed.

Definition at line 4192 of file DGraph.java.

References denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.BBType.CAP, denoptim.graph.Vertex.getAP(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), and denoptim.graph.Vertex.newVertexFromLibrary().

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◆ addEdge()

void denoptim.graph.DGraph.addEdge ( Edge edge )

Adds the edge to the list of edges belonging to this graph.

Parameters

edge	to be included in the list of edges

Definition at line 1021 of file DGraph.java.

References denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

◆ addRing() [1/3]

void denoptim.graph.DGraph.addRing ( Ring ring )

Definition at line 1030 of file DGraph.java.

References denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

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◆ addRing() [2/3]

void denoptim.graph.DGraph.addRing	(	Vertex	vI,
		Vertex	vJ
	)		throws DENOPTIMException

Adds a chord between the given vertices, thus adding a ring in this graph.

Parameters

vI	one of the ring-closing vertices.
vJ	the other of the ring-closing vertices.

Exceptions

DENOPTIMException if the two vertices do not have consistent bond types to their parents and, therefore, we cannot infer the bond type of the chord.

Definition at line 1047 of file DGraph.java.

References denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

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◆ addRing() [3/3]

void denoptim.graph.DGraph.addRing	(	Vertex	vI,
		Vertex	vJ,
		BondType	bndTyp
	)

Adds a chord between the given vertices, thus adding a ring in this graph.

Parameters

vI	one of the ring-closing vertices.
vJ	the other of the ring-closing vertices.
bndTyp	the bond type the chord corresponds to.

Definition at line 1075 of file DGraph.java.

References denoptim.graph.DGraph.addRing(), denoptim.graph.rings.PathSubGraph.getVertecesPath(), denoptim.graph.DGraph.jGraph, denoptim.graph.DGraph.jGraphKernel, and denoptim.graph.Ring.setBondType().

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◆ addSymmetricSetOfVertices()

void denoptim.graph.DGraph.addSymmetricSetOfVertices ( SymmetricVertexes symSet ) throws DENOPTIMException

Adds a symmetric set of vertices to this graph.

Parameters

symSet the set to add

Exceptions

DENOPTIMException is the symmetric set being added contains an id that is already contained in another set already present.

Definition at line 661 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

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◆ addVertex()

void denoptim.graph.DGraph.addVertex ( Vertex vertex ) throws DENOPTIMException

Appends a vertex to this graph without creating any edge.

This is a good way to add the first vertex, but can be used also if you intend to add edges manually.

Parameters

vertex the vertex that will be added (no cloning).

Exceptions

DENOPTIMException in the vertex has an ID that is already present in the current list of vertices of this graph, if any.

Definition at line 1097 of file DGraph.java.

References denoptim.graph.DGraph.containsVertexID(), denoptim.graph.DGraph.getGraphId(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

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◆ appendGraphOnAP() [1/2]

void denoptim.graph.DGraph.appendGraphOnAP	(	AttachmentPoint	apOnThisGraph,
		AttachmentPoint	apOnIncomingGraph,
		BondType	bndType
	)		throws DENOPTIMException

Appends a graph onto this graph.

The operation is not projected by symmetry, and the incoming graph is not cloned/copied.

Parameters

apOnThisGraph	where to append to on this growing graph.
apOnIncomingGraph	where to connect this graph into the incoming one.
bndType	the bond type of the new edge created.

Exceptions

DENOPTIMException

Definition at line 5826 of file DGraph.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addRing(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.cleanup(), denoptim.graph.DGraph.getEdgeList(), denoptim.graph.DGraph.getRings(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.DGraph.renumberGraphVertices().

Referenced by denoptim.graph.DGraph.appendGraphOnGraph().

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◆ appendGraphOnAP() [2/2]

void denoptim.graph.DGraph.appendGraphOnAP	(	Vertex	parentVertex,
		int	parentAPIdx,
		DGraph	subGraph,
		Vertex	childVertex,
		int	childAPIdx,
		BondType	bndType,
		Map< Vertex, SymmetricVertexes >	newSymSets
	)		throws DENOPTIMException

Append a subgraph (I) to this graph (R) specifying which vertex and attachment point to use for the connection.

Does not project on symmetrically related vertices or attachment points. No change in symmetric sets, apart from importing those sets that are already defined in the subgraph.

Parameters

parentVertex	the vertex of R on which a copy of I is to be attached.
parentAPIdx	the attachment point on R's vertex to be used to attach I
subGraph	the incoming graph I, or child graph.
childVertex	the vertex of I that is to be connected to R
childAPIdx	the index of the attachment point on the vertex of I that is to be connected to R
bndType	the bond type between R and I
newSymSets	of symmetric sets. This parameter is only used to keep track of the symmetric copies of I. Simply provide an empty data structure.

Definition at line 5880 of file DGraph.java.

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◆ appendGraphOnGraph() [1/2]

void denoptim.graph.DGraph.appendGraphOnGraph	(	List< Vertex >	parentVertices,
		List< Integer >	parentAPIdx,
		DGraph	subGraph,
		Vertex	childVertex,
		int	childAPIdx,
		BondType	bndType,
		boolean	onAllSymmAPs
	)		throws DENOPTIMException

Append a graph (incoming=I) onto this (receiving=R).

Can append one or more copies of the same graph. The corresponding vertex and attachment point ID for each connection are given in separated arrays.

Parameters

parentVertices	the list of source vertices of R on which a copy of I is to be attached.
parentAPIdx	the list of attachment points on R's vertices to be used to attach I
subGraph	the incoming graph I, or child
childVertex	the vertex of I that is to be connected to R
childAPIdx	the index of the attachment point on the vertex of I that is to be connected to R
bndType	the bond type between R and I
onAllSymmAPs	set to `true` to require the same graph I to be attached on all available and symmetric APs on the same vertex of the AP indicated in the list.

Definition at line 5743 of file DGraph.java.

References denoptim.graph.DGraph.appendGraphOnGraph().

Referenced by denoptim.graph.DGraph.appendGraphOnGraph(), and denoptim.graph.DGraph.editGraph().

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◆ appendGraphOnGraph() [2/2]

void denoptim.graph.DGraph.appendGraphOnGraph	(	Vertex	parentVertex,
		int	parentAPIdx,
		DGraph	subGraph,
		Vertex	childVertex,
		int	childAPIdx,
		BondType	bndType,
		Map< Vertex, SymmetricVertexes >	newSymSets,
		boolean	onAllSymmAPs
	)		throws DENOPTIMException

Append a graph (incoming=I) onto this graph (receiving=R).

Parameters

parentVertex	the vertex of R on which the a copy of I is to be attached.
parentAPIdx	the attachment point on R's vertex to be used to attach I
subGraph	the incoming graph I, or child
childVertex	the vertex of I that is to be connected to R
childAPIdx	the index of the attachment point on the vertex of I that is to be connected to R
bndType	the bond type between R and I
newSymSets	this parameter is only used to keep track of the symmetric copies of I. Simply provide an empty data structure.
onAllSymmAPs	set to `true` to require the same graph I to be attached on all available and symmetric APs on the same vertex of the AP indicated in the list.

Definition at line 6005 of file DGraph.java.

References denoptim.graph.DGraph.appendGraphOnAP().

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◆ appendVertexOnAP()

void denoptim.graph.DGraph.appendVertexOnAP	(	AttachmentPoint	srcAP,
		AttachmentPoint	trgAP
	)		throws DENOPTIMException

Append a vertex to this graph: adds the new vertex to the list of vertices belonging to the graph, and adds the resulting edge to the graph.

Does not clone the incoming vertex. Does not project on symmetrically related vertices or attachment points. No change in symmetric sets, apart from importing those sets that are already defined in the incoming vertex.

Parameters

srcAP	the attachment point on this graph (source AP).
trgAP	the attachment point on the incoming vertex (target AP).

Exceptions

DENOPTIMException

Definition at line 5776 of file DGraph.java.

References denoptim.graph.DGraph.addEdge(), denoptim.graph.DGraph.addVertex(), denoptim.graph.Edge.BondType.ANY, and denoptim.graph.Edge.BondType.UNDEFINED.

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◆ areApsUsedBySymmetricUsers()

static boolean denoptim.graph.DGraph.areApsUsedBySymmetricUsers	(	AttachmentPoint	apA,
		AttachmentPoint	apB,
		Set< Vertex >	alreadyAssignedVrtxs
	)

static

Checks if the Vertexs that are attached to two given AttachmentPoints apA and apB satisfy these conditions:

the linked APs must return true from AttachmentPoint#sameAs(AttachmentPoint)
the Vertex owner of apB is not contained in the set of already-assigned vertexes (the 3rd argument)
the Vertexa attached to apA andapB must be return satisfy Vertex#sameAs(Vertex)
if such vertexes are instances of Fragment, then they must
satisfy Fragment#isIsomorphicTo(Vertex).

These conditions, when satisfied for a pair of used and symmetric AttachmentPoints apA and apB should suffice to assign the two user Vertexs to the same SymmetricVertexes set.

Parameters

apA	one attachment point in the pair.
apB	the other attachment point in the pair.
alreadyAssignedVrtxs	a set of vertexes that have been already assigned to `SymmetricVertexes` set.

Returns

Definition at line 565 of file DGraph.java.

References denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Fragment.isIsomorphicTo(), denoptim.graph.AttachmentPoint.sameAs(), and denoptim.graph.Vertex.sameAs().

Referenced by denoptim.graph.DGraph.detectSymVertexSets(), and denoptim.graph.DGraph.findSymmetrySetsOfChildVertexes().

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◆ changeSignOfVertexID()

void denoptim.graph.DGraph.changeSignOfVertexID ( )

Change all vertex IDs to the corresponding negative value.

For instance if the vertex ID is 12 this method changes it into -12.

Definition at line 5252 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getEdgeList(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.Edge.getTrgAP(), denoptim.graph.Edge.getTrgVertex(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.Vertex.setVertexId().

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◆ checkConsistency() [1/2]

Object[] denoptim.graph.DGraph.checkConsistency ( RunTimeParameters settings ) throws DENOPTIMException

Peeks into this graph to derive a preliminary chemical representation with SMILES and InChIKey.

The chemical entity is evaluated also against the criteria defined by the given settings WARNING Although Cartesian coordinates are assigned to each atom and pseudo-atom in the molecular representation, such coordinates do NOT represent a valid 3D model. As a consequence stereochemical descriptors in the INCHI representation are not consistent with the actual arrangement of fragments.

Parameters

settings the collection of settings defining the criteria with which we evaluate the graph.

Returns: an object array containing the InChI key, the SMILES string and the 2D representation of the molecule. null is returned if any check or conversion fails.

Exceptions

DENOPTIMException

Definition at line 5353 of file DGraph.java.

References denoptim.graph.DGraph.checkConsistency().

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.graph.DGraph.checkConsistency(), and denoptim.ga.EAUtils.readCandidateFromFile().

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◆ checkConsistency() [2/2]

Object[] denoptim.graph.DGraph.checkConsistency	(	RunTimeParameters	settings,
		boolean	permissive
	)		throws DENOPTIMException

Peeks into this graph to derive a preliminary chemical representation with SMILES and InChIKey.

The chemical entity is evaluated also against the criteria defined by the given settings WARNING Although Cartesian coordinates are assigned to each atom and pseudo-atom in the molecular representation, such coordinates do NOT represent a valid 3D model. As a consequence stereochemical descriptors in the INCHI representation are not consistent with the actual arrangement of fragments.

Parameters

settings	the collection of settings defining the criteria with which we evaluate the graph.
permissive	use `true` to ignore some of the most strict filtering criteria. This is typically done only when reading graphs from the user, thus assuming the user does intend to by-pass some filters when inspecting a graph that might not be possible to generate from the given settings,

Returns: an object array containing the InChI key, the SMILES string and the 2D representation of the molecule. null is returned if any check or conversion fails.

Exceptions

DENOPTIMException

Definition at line 5384 of file DGraph.java.

References denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.utils.MoleculeUtils.getHeavyAtomCount(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), denoptim.fragspace.FragmentSpaceParameters.getMaxHeavyAtom(), denoptim.fragspace.FragmentSpaceParameters.getMaxMW(), denoptim.graph.rings.RingClosureParameters.getMaxRcaPerType(), denoptim.fragspace.FragmentSpaceParameters.getMaxRotatableBond(), denoptim.graph.rings.RingClosureParameters.getMinRcaPerType(), denoptim.graph.rings.RingClosureParameters.getMinRingClosures(), denoptim.utils.MoleculeUtils.getMolecularWeight(), denoptim.utils.MoleculeUtils.getNumberOfRotatableBonds(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.DGraph.getRCVertices(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.DGraph.hasForbiddenEnd(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.rings.RingClosingAttractor.RCATYPEMAP, denoptim.molecularmodeling.ThreeDimTreeBuilder.setAlignBBsIn3D(), denoptim.graph.DGraph.toString(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

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◆ cleanup()

void denoptim.graph.DGraph.cleanup ( )

Wipes the data in this graph.

Definition at line 3368 of file DGraph.java.

References denoptim.graph.DGraph.closableChains, denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.jGraph, denoptim.graph.DGraph.jGraphKernel, and denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.DGraph.appendGraphOnAP(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.graph.Candidate.cleanup(), denoptim.ga.EAUtils.readCandidateFromFile(), and denoptim.task.FitnessTask.runExternalFitness().

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◆ clone()

DGraph denoptim.graph.DGraph.clone ( )

Returns almost "deep-copy" of this graph.

Only the APCLass members of member of this class should remain references to the original APClasses. The vertex IDs are not changed, so you might want to renumber the graph.

Definition at line 3186 of file DGraph.java.

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◆ compareGraphNodes() [1/2]

static boolean denoptim.graph.DGraph.compareGraphNodes	(	Vertex	seedOnA,
		DGraph	gA,
		Vertex	seedOnB,
		DGraph	gB,
		Map< Vertex, Vertex >	vertexMap,
		StringBuilder	reason
	)		throws DENOPTIMException

staticprivate

Compares graphs by spanning vertices starting from the given vertex and following the direction of edges.

Parameters

seedOnA	initial vertex on the first graph.
gA	the first graph.
seedOnB	initial vertex on the second graph.
gB	the second graph.
vertexMap	vertex mapping.
reason	a string recording the reason for returning false.

Returns: true if the graphs are same at this node.

Exceptions

DENOPTIMException

Definition at line 3849 of file DGraph.java.

References denoptim.graph.DGraph.compareGraphNodes(), and denoptim.graph.Edge.getTrgVertex().

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◆ compareGraphNodes() [2/2]

static boolean denoptim.graph.DGraph.compareGraphNodes	(	Vertex	thisV,
		DGraph	thisG,
		Vertex	otherV,
		DGraph	otherG
	)		throws DENOPTIMException

static

Compares graphs by spanning vertices starting from the given vertex and following the direction of edges.

Parameters

thisV	starting vertex of first graph
thisG	first graph
otherV	starting vertex of second graph
otherG	second graph

Returns: true if the graphs are same at this node

Exceptions

DENOPTIMException

Definition at line 3825 of file DGraph.java.

References denoptim.graph.DGraph.compareGraphNodes().

Referenced by denoptim.graph.DGraph.compareGraphNodes(), denoptim.graph.DGraph.sameAs(), and denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem().

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◆ containsAtoms()

boolean denoptim.graph.DGraph.containsAtoms ( )

Returns true if this graph has any vertex that contains atoms.

Returns: true if this graph has any vertex that contains atoms.

Definition at line 3935 of file DGraph.java.

References denoptim.graph.DGraph.getVertexList().

Referenced by denoptim.graph.Template.containsAtoms(), and denoptim.gui.GraphVertexMolViewerPanel.updateMolevularViewer().

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◆ containsOrEmbedsVertex()

boolean denoptim.graph.DGraph.containsOrEmbedsVertex ( Vertex v )

Check if the specified vertex is contained in this graph as a node or in any inner graphs that may be embedded in Template-kind vertex belonging to this graph.

Parameters

v	the vertex.

Returns: true if the vertex belongs to this graph or is anyhow embedded in it.

Definition at line 2530 of file DGraph.java.

References denoptim.graph.DGraph.containsOrEmbedsVertex(), denoptim.graph.Template.getInnerGraph(), and denoptim.graph.DGraph.gVertices.

Referenced by denoptim.ga.EAUtils.buildGraph(), and denoptim.graph.DGraph.containsOrEmbedsVertex().

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◆ containsVertex()

boolean denoptim.graph.DGraph.containsVertex ( Vertex v )

Check if this graph contains the specified vertex.

Does not consider inner graphs that may be embedded in Template-kind vertex belonging to this graph.

Parameters

v	the vertex.

Returns: true if the vertex belongs to this graph.

Definition at line 2557 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.DGraph.replaceSingleSubGraph(), denoptim.graph.DGraphTest.testRemoveCapping(), and denoptim.graph.DGraphTest.testReplaceVertex().

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◆ containsVertexID()

boolean denoptim.graph.DGraph.containsVertexID ( long l )

Checks if a number is already used as VertexIDs within the graph.

Returns: true if the number is already used.

Definition at line 3349 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.addVertex().

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◆ convertSymmetricLabelsToSymmetricSets()

void denoptim.graph.DGraph.convertSymmetricLabelsToSymmetricSets ( )

protected

Looks for any symmetric labels, creates symmetric sets that collect the same information, and removes the original symmetric labels.

Definition at line 1600 of file DGraph.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.hasSymmetryInvolvingVertex(), and denoptim.constants.DENOPTIMConstants.VRTSYMMSETID.

Referenced by denoptim.graph.DGraph.replaceSubGraph(), denoptim.graph.DGraph.replaceVertex(), denoptim.graph.DGraphTest.testConvertSymmetricLabelsToSymmetricSets(), and denoptim.graph.DGraphTest.testReplaceSubGraph().

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◆ detectSymVertexSets()

boolean denoptim.graph.DGraph.detectSymVertexSets ( ) throws DENOPTIMException

Tries to determine the set of symmetric vertices in this graph based on finding compatible Vertexes that are either using symmetric AttachmentPoints (NB: all symmetric APs must be in use by vertexes that are compatible with each other) or that are downstream (i.e., according to edge direction) w.r.t Vertexes that are using symmetric AttachmentPoints.The compatibility of the vertexes is determined by these criteria:

the AP used to link the parent vertex must have the same features as defined by the AttachmentPoint#sameAs(Vertex) method.
the vertex must have the same features as defined by the Vertex#sameAs(Vertex) method. Effectively, this means they are instances of the same building block in the fragment space, or are graph building blocks that are not part of the fragment space, in which case the last condition applies,
vertexes have same features and isomorphic internal structure as from the Fragment#isIsomorphicTo(Vertex) method.

Returns: true if some symmetric set of vertex has been found.

Exceptions

DENOPTIMException

Definition at line 372 of file DGraph.java.

References denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.graph.DGraph.areApsUsedBySymmetricUsers(), denoptim.graph.DGraph.findSymmetrySetsOfChildVertexes(), denoptim.graph.SymmetricAPs.getAllSameAs(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.DGraph.symVertices.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.graph.DGraphTest.testDetectSymVertexSets().

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◆ directedPathExists()

boolean denoptim.graph.DGraph.directedPathExists	(	Vertex	src,
		Vertex	trg
	)

Uses branch identifiers to define is two vertices are in such a relation that allows the drawing of a directed path from one to the other.

You must run getChildrenTree(Vertex, List, AtomicInteger, List) on any parent of either graph to generate the bran branch labeling.

Parameters

src	the "from" in the directed path relation.
trg	the "to" in the directed path relation.

Returns: true if the relation exists, false is if doesn't OR if the branch labeling has not been found.

Definition at line 3000 of file DGraph.java.

References denoptim.graph.DGraph.getBranchIdOfVertex().

Referenced by denoptim.graph.DGraphTest.testGetChildrenTreeWithBranchIdentifier().

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◆ editGraph()

DGraph denoptim.graph.DGraph.editGraph	(	ArrayList< GraphEdit >	edits,
		boolean	symmetry,
		FragmentSpace	fragSpace,
		Logger	logger
	)		throws DENOPTIMException

Edit this graph according to a given list of edit tasks.

This method assumes the vertex IDs are unique.

Parameters

edits	the list of edit tasks.
symmetry	if `true` the same operation is performed on vertices related by symmetry.
fragSpace	the space of building blocks needed to perform the graph editing tasks. It may or may not be the space that generated the original version of the graph to edit.
logger	the logger to use

Returns: the modified graph.

Definition at line 6453 of file DGraph.java.

Referenced by denoptim.programs.grapheditor.GraphEditor.runProgram().

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◆ embedPatternsInTemplates() [1/2]

DGraph denoptim.graph.DGraph.embedPatternsInTemplates	(	GraphPattern	pattern,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Searches for the given pattern type and generated a new graph where each set of (clones of) vertexes that define one such patterns is embedded in a single template.

Parameters

pattern type of pattern to embed in template.

Returns: a new graph where the vertexes defining each pattern are replaced by a template that embeds the subgraph of the pattern.

Exceptions

DENOPTIMException

Definition at line 4616 of file DGraph.java.

References denoptim.graph.DGraph.embedPatternsInTemplates(), and denoptim.graph.Template.ContractLevel.FREE.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.DGraphTest.testEmbedPatternsInTemplates(), and denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol().

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◆ embedPatternsInTemplates() [2/2]

DGraph denoptim.graph.DGraph.embedPatternsInTemplates	(	GraphPattern	pattern,
		FragmentSpace	fragSpace,
		ContractLevel	contract
	)		throws DENOPTIMException

Searches for the given pattern type and generated a new graph where each set of (clones of) vertexes that define one such patterns is embedded in a single template.

Parameters

pattern	type of pattern to embed in template.
fragSpace	the fragment space that defines how we manipulate fragments.
contract	the level of constraint to set for any template that embeds one of the patterns.

Returns: a new graph where the vertexes defining each pattern are replaced by a template that embeds the subgraph of the pattern.

Exceptions

DENOPTIMException

Definition at line 4637 of file DGraph.java.

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◆ ensureUniqueApIDs()

void denoptim.graph.DGraph.ensureUniqueApIDs ( )

protected

Definition at line 6669 of file DGraph.java.

References denoptim.graph.DGraph.apCounter, and denoptim.graph.DGraph.getAttachmentPoints().

Referenced by denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.DGraph.DENOPTIMGraphSerializer.serialize(), and denoptim.graph.Template.toJson().

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◆ extractPattern() [1/2]

List< DGraph > denoptim.graph.DGraph.extractPattern ( GraphPattern pattern ) throws DENOPTIMException

Extracts subgraphs that match the provided pattern.

Parameters

pattern to match against.

Returns: The subgraphs matching the provided pattern. These contain clones of the vertexes in this graph.

Exceptions

DENOPTIMException

Definition at line 4457 of file DGraph.java.

References denoptim.graph.DGraph.extractPattern().

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.graph.DGraph.extractPattern(), denoptim.ga.GraphOperationsTest.testExtractPattern_fusedRings(), denoptim.ga.GraphOperationsTest.testExtractPattern_returnsEmptyListIfNoRings(), and denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem().

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◆ extractPattern() [2/2]

Map< DGraph, ObjectPair > denoptim.graph.DGraph.extractPattern	(	GraphPattern	pattern,
		boolean	recordConnectivity
	)		throws DENOPTIMException

Extracts subgraphs that match the provided pattern.

This method offers the possibility to record the connections that cross the border of each subgraph.

Parameters

pattern	to match against.
recordConnectivity	if `true` makes this method collect the edges of this graph that cross the subgraph borders. If `false` the resulting map will have only keys and `null` values.

Returns: The subgraphs matching the provided pattern. Each such subgraph contains clones of the vertexes in this graph. Each value of the returned map contains two lists defining which edges cross the subgraph border: first, the list of incoming edges (i.e., the source AttachmentPoint belongs to a vertex that does not belong the subgraph), second, the list of outgoing edges (i.e., the source AttachmentPoint belongs to a vertex that does belong the subgraph). Note that the owners of the AttachmentPoints are NOT the Vertex instances that are container in the map's key, but are their clones.

Exceptions

DENOPTIMException

Definition at line 4488 of file DGraph.java.

References denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.Ring.getVertices(), denoptim.graph.DGraph.reorderVertexList(), denoptim.graph.GraphPattern.RING, and denoptim.utils.GeneralUtils.unionOfIntersectingSets().

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◆ extractSubgraph() [1/7]

DGraph denoptim.graph.DGraph.extractSubgraph ( Collection< Vertex > definedOn )

Returns a clone of the subgraph defined by the a collection of vertices belonging to this graph.

Parameters

definedOn Set of vertices that defined the subgraph.

Returns: a clone of the subgraph of this graph.

Definition at line 4539 of file DGraph.java.

References denoptim.graph.DGraph.extractSubgraph().

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◆ extractSubgraph() [2/7]

DGraph denoptim.graph.DGraph.extractSubgraph	(	Collection< Vertex >	definedOn,
		Set< Edge >	connectionToSubgraph,
		Set< Edge >	connectionFromSubgraph
	)

Returns a clone of the subgraph defined by the a collection of vertices belonging to this graph.

It also collects which Edges exists between the subgraph and the rest of the graph.

Parameters

definedOn	Set of vertices that defined the subgraph.
connectionToSubgraph	container for the collection of edges that arrive at the subgraph.
connectionFromSubgraph	container for the collection of edges that depart from the subgraph.

Returns: Subgraph of graph defined on set of vertices.

Definition at line 4558 of file DGraph.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.getEdgeList(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.DGraph.removeVertex().

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◆ extractSubgraph() [3/7]

DGraph denoptim.graph.DGraph.extractSubgraph ( int index ) throws DENOPTIMException

Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex.

Only the seed vertex and all child vertices (and further successors) are considered part of the subgraph, which includes also rings and symmetric sets. All rings that include vertices not belonging to the subgraph are lost.

Parameters

index the position of the seed vertex in the list of vertices of this graph.

Returns: a new graph that corresponds to the subgraph of this graph.

Definition at line 4258 of file DGraph.java.

References denoptim.graph.DGraph.extractSubgraph(), and denoptim.graph.DGraph.getVertexAtPosition().

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.graph.DGraph.extractPattern(), denoptim.graph.DGraph.extractSubgraph(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.ga.GraphOperations.performCrossover(), denoptim.ga.GraphOperations.processPermutationOfEndPoints(), denoptim.graph.DGraphTest.testExtractSubgraph(), and denoptim.graph.DGraphTest.testExtractSubgraphFromCollection().

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◆ extractSubgraph() [4/7]

DGraph denoptim.graph.DGraph.extractSubgraph ( Vertex seed ) throws DENOPTIMException

Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex.

Only the seed vertex and all child vertices (and further successors) are considered part of the subgraph, which includes also rings and symmetric sets. All rings that include vertices not belonging to the subgraph are lost.

Parameters

seed	the vertex from which the extraction has to start.

Returns: a new graph that corresponds to the subgraph of this graph.

Definition at line 4277 of file DGraph.java.

References denoptim.graph.DGraph.extractSubgraph().

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◆ extractSubgraph() [5/7]

DGraph denoptim.graph.DGraph.extractSubgraph	(	Vertex	seed,
		boolean	stopBeforeRCVs
	)		throws DENOPTIMException

Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex.

Optionally, you can ask to stop the exploration of a branch before including any ring-closing vertex. Only the seed vertex and all child vertices (and further successors) are considered part of the subgraph, which includes also rings and symmetric sets. All rings that include vertices not belonging to the subgraph are lost.

Parameters

seed	the vertex from which the extraction has to start.
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Returns: a new graph that corresponds to the subgraph of this graph.

Definition at line 4414 of file DGraph.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.getChildTreeLimited(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.indexOf(), and denoptim.graph.DGraph.removeVertex().

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◆ extractSubgraph() [6/7]

DGraph denoptim.graph.DGraph.extractSubgraph	(	Vertex	seed,
		int	numLayers,
		boolean	stopBeforeRCVs
	)		throws DENOPTIMException

Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex and visiting at most a given number of vertex layers, and optionally stopping the exploration of a branch before including any ring-closing vertex.

Only the seed vertex and all child vertices (and further successors) are considered part of the subgraph, which includes also rings and symmetric sets. All rings that include vertices not belonging to the subgraph are lost.

Parameters

seed	the vertex from which the extraction has to start.
numLayers	the maximum number of vertex layers after the seen vertex that we want to consider before stopping. If this value is 2, we will explore three layers: the seed, and two more layers away from it.
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Returns: a new graph that corresponds to the subgraph of this graph.

Definition at line 4303 of file DGraph.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.indexOf(), and denoptim.graph.DGraph.removeVertex().

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◆ extractSubgraph() [7/7]

DGraph denoptim.graph.DGraph.extractSubgraph	(	Vertex	seed,
		List< Vertex >	limits,
		boolean	stopBeforeRCVs
	)		throws DENOPTIMException

Creates a new graph that corresponds to the subgraph of this graph when exploring the spanning tree from a given seed vertex and stopping the exploration at the given end vertices (i.e., limits).

Optionally, you can ask to stop the exploration of a branch before including any ring-closing vertex. Only the seed vertex and all child vertices (and further successors) are considered part of the subgraph, which includes also rings and symmetric sets. All rings that include vertices not belonging to the subgraph are lost.

Parameters

seed	the vertex from which the extraction has to start.
limits	the vertices playing the role of subgraph end-points that stop the exploration of the graph.
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Returns: a new graph that corresponds to the subgraph of this graph.

Definition at line 4354 of file DGraph.java.

References denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getChildTreeLimited(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.indexOf(), and denoptim.graph.DGraph.removeVertex().

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◆ findSymmetrySetsOfChildVertexes()

Map< SymmetricAPs, List< Vertex > > denoptim.graph.DGraph.findSymmetrySetsOfChildVertexes	(	Vertex	vrtx,
		Set< Vertex >	alreadyAssignedVrtxs
	)

package

Definition at line 460 of file DGraph.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.areApsUsedBySymmetricUsers(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getLinkedAPThroughout(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Vertex.getSymmetricAPSets().

Referenced by denoptim.graph.DGraph.detectSymVertexSets(), and denoptim.graph.DGraphTest.testFindSymmetrySetsOfChildVertexes().

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◆ findVertices() [1/2]

ArrayList< Vertex > denoptim.graph.DGraph.findVertices	(	VertexQuery	vrtxQuery,
		boolean	purgeSym,
		Logger	logger
	)

Filters a list of vertices according to a query.

vertex.

Parameters

vrtxQuery	the query defining what is that we want to find.
purgeSym	use `true` to remove symmetrically redundant matches.
logger	manager of log

Returns: the list of vertices that match the query.

Definition at line 6079 of file DGraph.java.

References denoptim.graph.DGraph.EdgeFinder.apply(), denoptim.graph.EdgeQuery.getBondType(), denoptim.graph.VertexQuery.getInEdgeQuery(), denoptim.graph.DGraph.getLevel(), denoptim.graph.VertexQuery.getOutEdgeQuery(), denoptim.graph.EdgeQuery.getSourceAPClass(), denoptim.graph.EdgeQuery.getSourceAPIdx(), denoptim.graph.EdgeQuery.getSourceVertexId(), denoptim.graph.EdgeQuery.getTargetAPClass(), denoptim.graph.EdgeQuery.getTargetAPIdx(), denoptim.graph.EdgeQuery.getTargetVertexId(), denoptim.graph.VertexQuery.getVertexBBIDQuery(), denoptim.graph.VertexQuery.getVertexBBTypeQuery(), denoptim.graph.VertexQuery.getVertexIDQuery(), denoptim.graph.VertexQuery.getVertexLevelQuery(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.VertexQuery.getVertexTypeQuery(), and denoptim.graph.DGraph.removeSymmetryRedundance().

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◆ findVertices() [2/2]

ArrayList< Vertex > denoptim.graph.DGraph.findVertices	(	VertexQuery	vrtxQuery,
		Logger	logger
	)

Filters a list of vertices according to a query.

vertex. Always removed symmetry-redundant matches.

Parameters

vrtxQuery	the query defining what is that we want to find.
logger	manager of log

Returns: the list of vertices that match the query.

Definition at line 6062 of file DGraph.java.

References denoptim.graph.DGraph.findVertices().

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.findVertices(), denoptim.graph.DGraph.findVerticesIds(), and denoptim.graph.DGraphTest.testFindVertex().

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◆ findVerticesIds()

List< Long > denoptim.graph.DGraph.findVerticesIds	(	VertexQuery	query,
		Logger	logger
	)

Search a graph for vertices that match the criteria defined in a query vertex.

Parameters

query	the query
logger	manager of log

Returns: the list of matches

Definition at line 6042 of file DGraph.java.

References denoptim.graph.DGraph.findVertices().

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◆ fixEdgeDirections() [1/2]

static void denoptim.graph.DGraph.fixEdgeDirections ( DGraph graph )

staticprivate

Flips edges in the graph so that the scaffold is the only source vertex.

Parameters

graph to fix edges of.

Definition at line 4733 of file DGraph.java.

References denoptim.graph.DGraph.fixEdgeDirections(), and denoptim.graph.DGraph.getSourceVertex().

Referenced by denoptim.graph.DGraph.fixEdgeDirections(), and denoptim.graph.DGraph.reorderVertexList().

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◆ fixEdgeDirections() [2/2]

static void denoptim.graph.DGraph.fixEdgeDirections	(	Vertex	v,
		Set< Long >	visited
	)

staticprivate

Recursive utility method for fixEdgeDirections(graph).

Parameters

v	current vertex

Definition at line 4745 of file DGraph.java.

References denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.Edge.flipEdge(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getEdgeUser(), denoptim.graph.Vertex.getNumberOfAPs(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.Edge.getTrgAP(), denoptim.graph.Edge.getTrgVertex(), and denoptim.graph.Vertex.getVertexId().

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◆ fromJson() [1/2]

static DGraph denoptim.graph.DGraph.fromJson ( Reader reader )

static

Reads a JSON string and returns an instance of this class.

Parameters

json	the string to parse.

Returns: a new instance of this class.

Definition at line 6700 of file DGraph.java.

References denoptim.graph.DGraph.fromJson(), and denoptim.json.DENOPTIMgson.getReader().

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◆ fromJson() [2/2]

static DGraph denoptim.graph.DGraph.fromJson ( String json )

static

Reads a JSON string and returns an instance of this class.

Parameters

json	the string to parse.

Returns: a new instance of this class.

Definition at line 6685 of file DGraph.java.

References denoptim.graph.DGraph.fromJson(), and denoptim.json.DENOPTIMgson.getReader().

Referenced by denoptim.graph.DGraph.DENOPTIMGraphDeserializer.deserialize(), denoptim.graph.DGraph.fromJson(), denoptim.graph.Template.fromJson(), denoptim.io.DenoptimIO.readDENOPTIMGraphsFromJSONFile(), denoptim.io.DenoptimIO.readGraphFromSDFileIAC(), and denoptim.graph.DGraphTest.testFromToJSON().

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◆ getAPOnLeftVertexID()

AttachmentPoint denoptim.graph.DGraph.getAPOnLeftVertexID	(	long	nbrVid,
		long	vid
	)

Finds the AP that is on the first given parameter and that is used to make a connection to the second vertex, no matter the direction of the edge.

If the two vertices are connected by a chord, i.e., there is a pair of RCVs in between the two vertices, we still work out the AP on the vertex on the left, even if in the graph it is actually used to bind the RCV that defines the chord and that eventually connects the vertex on the left with that on the right.

Parameters

nbrVid	vertex ID of one vertex.
vid	vertex ID of another vertex.

Returns: the AttachmentPoint or null is the two vertex IDs are not connected in this graph.

Definition at line 7005 of file DGraph.java.

References denoptim.graph.DGraph.getChildVertices(), denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getTrgAP(), and denoptim.graph.DGraph.getVertexWithId().

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◆ getAPWithId()

AttachmentPoint denoptim.graph.DGraph.getAPWithId ( int id )

Returns the attachment point with the given identifier, or null if no AP is found with the given identifier.

Parameters

id	identifier of the attachment point to return

Returns: the attachment point with the given identifier, or null if no AP is found with the given identifier.

Definition at line 4035 of file DGraph.java.

References denoptim.graph.DGraph.getAttachmentPoints().

Referenced by denoptim.graph.DGraph.DENOPTIMGraphDeserializer.deserialize(), denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.embedPatternsInTemplates(), and denoptim.graph.Template.updateInnerToOuter().

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◆ getAttachmentPoints()

ArrayList< AttachmentPoint > denoptim.graph.DGraph.getAttachmentPoints ( )

Returns the list of all attachment points contained in this graph.

Returns: list of attachment points.

Definition at line 3970 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.ensureUniqueApIDs(), denoptim.graph.DGraph.getAPWithId(), denoptim.graph.DGraph.getAvailableAPs(), denoptim.graph.DGraph.getAvailableAPsThroughout(), and denoptim.ga.EAUtilsTest.testCrowdingProbability().

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◆ getAvailableAPs()

ArrayList< AttachmentPoint > denoptim.graph.DGraph.getAvailableAPs ( )

Returns the list of available attachment points contained in this graph.

Returns: list of attachment points.

Definition at line 3988 of file DGraph.java.

References denoptim.graph.DGraph.getAttachmentPoints().

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.utils.GraphConversionTool.getJGraphKernelFromGraph(), denoptim.graph.Template.isValidInnerGraph(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.Template.setInnerGraph(), denoptim.graph.DGraphTest.testGetAvailableAPs_returnsListOfAvailableAPs(), and denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

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◆ getAvailableAPsThroughout()

List< AttachmentPoint > denoptim.graph.DGraph.getAvailableAPsThroughout ( )

Returns the list of attachment points contained in this graph that are available throughout the template barrier, i.e., are free in this graph an in any embedding graph that containing this one.

Returns: list of attachment points.

Definition at line 4011 of file DGraph.java.

References denoptim.graph.DGraph.getAttachmentPoints().

Referenced by denoptim.ga.GraphOperations.addRing().

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◆ getBondingAPIndex()

int denoptim.graph.DGraph.getBondingAPIndex	(	Vertex	srcVert,
		int	dapidx,
		Vertex	dstVert
	)

Parameters

srcVert
dapidx	the AP corresponding to the source fragment
dstVert

Returns: the AP index of the destination fragment

Deprecated:: this depends on vertedID rather than reference

Definition at line 2725 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getEdgeList(), denoptim.graph.Edge.getSrcAPID(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.Edge.getTrgAPID(), denoptim.graph.Edge.getTrgVertex(), and denoptim.graph.Vertex.getVertexId().

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◆ getBranchIdOfVertex()

List< Integer > denoptim.graph.DGraph.getBranchIdOfVertex ( Vertex v )

Returns the branch identifier.

Parameters

i	the position of the vertex to analyze.

Returns: the branch identifier or null if the vertex does not belong to this graph or if such property is not available. In the latter case, you should run getChildrenTree(Vertex, List, AtomicInteger, List) on any of the parent vertices.

Definition at line 2958 of file DGraph.java.

References denoptim.constants.DENOPTIMConstants.GRAPHBRANCHID, and denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.directedPathExists(), denoptim.graph.DGraph.getBranchIdOfVertexAsStr(), and denoptim.graph.DGraph.getBranchIdOfVertexAtPosition().

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◆ getBranchIdOfVertexAsStr()

String denoptim.graph.DGraph.getBranchIdOfVertexAsStr ( Vertex v )

Returns the branch identifier as a literal string.

Parameters

i	the position of the vertex to analyze.

Returns: the branch identifier expressed as a string or null if the vertex does not belong to this graph or if such property is not available. In the latter case, you should run getChildrenTree(Vertex, List, AtomicInteger, List) on any of the parent vertices.

Definition at line 2978 of file DGraph.java.

References denoptim.graph.DGraph.getBranchIdOfVertex().

Referenced by denoptim.ga.GraphOperations.locateCompatibleXOverPoints().

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◆ getBranchIdOfVertexAtPosition()

List< Integer > denoptim.graph.DGraph.getBranchIdOfVertexAtPosition ( int i )

Returns the branch identifier.

Parameters

i	the position of the vertex to analyze.

Returns: the branch identifier or null if such property is not available. In such case, you should run getChildrenTree(Vertex, List, AtomicInteger, List) on any of the parent vertices.

Definition at line 2941 of file DGraph.java.

References denoptim.graph.DGraph.getBranchIdOfVertex(), and denoptim.graph.DGraph.getVertexAtPosition().

Referenced by denoptim.graph.DGraphTest.testGetChildrenTreeWithBranchIdentifier().

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◆ getCandidateOwner()

Candidate denoptim.graph.DGraph.getCandidateOwner ( )

Returns the reference of the candidate item that is defined by this graph.

Returns: the reference to the owner or null.

Definition at line 251 of file DGraph.java.

References denoptim.graph.DGraph.candidate.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), and denoptim.ga.EAUtils.buildCandidatesByXOver().

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◆ getChildrenTree() [1/4]

void denoptim.graph.DGraph.getChildrenTree	(	Vertex	vertex,
		List< Vertex >	children
	)

Gets all the children of the current vertex recursively.

This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children

Definition at line 2771 of file DGraph.java.

References denoptim.graph.DGraph.getChildrenTree(), and denoptim.graph.DGraph.getChildVertices().

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getChildrenTree(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.graph.DGraph.removeOrphanBranchStartingAt(), denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph(), denoptim.graph.DGraphTest.testGetChildrenTree(), and denoptim.graph.DGraphTest.testGetChildrenTreeWithBranchIdentifier().

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◆ getChildrenTree() [2/4]

void denoptim.graph.DGraph.getChildrenTree	(	Vertex	vertex,
		List< Vertex >	children,
		AtomicInteger	branchIdGenerator,
		List< Integer >	prevBranchId
	)

Gets all the children of the current vertex recursively.

All vertices belonging to the children tree are labelled by a property that identifies which branches they belong to (DENOPTIMConstants.GRAPHBRANCHID). This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
branchIdGenerator	the generator of branch identifiers
prevBranchId	the identifier of the branch holding the given `vertex` belongs.

Definition at line 2861 of file DGraph.java.

References denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getChildVertices(), and denoptim.constants.DENOPTIMConstants.GRAPHBRANCHID.

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◆ getChildrenTree() [3/4]

void denoptim.graph.DGraph.getChildrenTree	(	Vertex	vertex,
		List< Vertex >	children,
		boolean	markBranches
	)

Gets all the children of the current vertex recursively.

All vertices belonging to the children tree can be labelled by a property that identifies which branches they belong to (DENOPTIMConstants.GRAPHBRANCHID). This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
markBranches	`true` to set the `DENOPTIMConstants.GRAPHBRANCHID` property to vertices, including the initial one. `vertex` belongs.

Definition at line 2804 of file DGraph.java.

References denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getChildVertices(), denoptim.constants.DENOPTIMConstants.GRAPHBRANCHID, and denoptim.graph.Vertex.setProperty().

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◆ getChildrenTree() [4/4]

void denoptim.graph.DGraph.getChildrenTree	(	Vertex	vertex,
		List< Vertex >	children,
		int	numLayers,
		boolean	stopBeforeRCVs
	)

Gets all the children of the current vertex recursively.

This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
numLayers	the maximum number of vertex layers after the seen vertex that we want to consider before stopping. If this value is 2, we will explore three layers: the seed, and two more layers away from it.
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Definition at line 2906 of file DGraph.java.

References denoptim.graph.DGraph.getChildrenTree(), and denoptim.graph.DGraph.getChildVertices().

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◆ getChildTreeLimited() [1/3]

void denoptim.graph.DGraph.getChildTreeLimited	(	Vertex	vertex,
		List< Vertex >	children,
		boolean	stopBeforeRCVs
	)

Gets all the children of the current vertex recursively.

This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Definition at line 3028 of file DGraph.java.

References denoptim.graph.DGraph.getChildTreeLimited(), and denoptim.graph.DGraph.getChildVertices().

Referenced by denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getChildTreeLimited(), denoptim.graph.DGraph.getSymmetricSubGraphs(), denoptim.ga.GraphOperations.processPermutationOfEndPoints(), and denoptim.programs.genetweeker.GeneOpsRunner.runXOver().

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◆ getChildTreeLimited() [2/3]

void denoptim.graph.DGraph.getChildTreeLimited	(	Vertex	vertex,
		List< Vertex >	children,
		List< Vertex >	limitsInClone,
		boolean	stopBeforeRCVs
	)

Gets all the children of the current vertex recursively until it finds one of the vertices listed as limit.

This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
limitsInClone	the list of vertices where exploration should stop.
stopBeforeRCVs	set `true` to make the exploration of each branch stop before including ring closing vertices.

Definition at line 3092 of file DGraph.java.

References denoptim.graph.DGraph.getChildTreeLimited(), and denoptim.graph.DGraph.getChildVertices().

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◆ getChildTreeLimited() [3/3]

void denoptim.graph.DGraph.getChildTreeLimited	(	Vertex	vertex,
		List< Vertex >	children,
		Set< Vertex >	limits
	)

Gets all the children of the current vertex recursively until it finds one of the vertices listed as limit.

This method does not cross template boundaries, thus all children belong to the same graph.

Parameters

vertex	the vertex whose children are to be located
children	list containing the references to all the children
limits	the list of vertices where exploration should stop.

Definition at line 3060 of file DGraph.java.

References denoptim.graph.DGraph.getChildTreeLimited(), and denoptim.graph.DGraph.getChildVertices().

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◆ getChildVertices()

ArrayList< Vertex > denoptim.graph.DGraph.getChildVertices ( Vertex vertex )

Parameters

vertex the vertex for which the first level of child vertices need to be found.

Returns: list of child vertices.

Definition at line 2757 of file DGraph.java.

References denoptim.graph.Vertex.getChilddren().

Referenced by denoptim.graph.DGraph.getAPOnLeftVertexID(), denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getChildTreeLimited(), denoptim.graph.DGraph.removeCappingGroupsFromChilds(), and denoptim.graph.DGraph.removeCappingGroupsOn().

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◆ getClosableChains()

List< ClosableChain > denoptim.graph.DGraph.getClosableChains ( )

Definition at line 712 of file DGraph.java.

References denoptim.graph.DGraph.closableChains.

◆ getDeepestAmongThese()

Vertex denoptim.graph.DGraph.getDeepestAmongThese ( List< Vertex > list )

Identify the oldest ancestor (i.e., most great grandparent) in the given collection.

In case of two vertices being at the same level, this returns the first.

Returns: the vertex that has the shortest path to the source.

Definition at line 3123 of file DGraph.java.

References denoptim.graph.DGraph.getParentTree().

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites().

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◆ getEdgeAtPosition()

Edge denoptim.graph.DGraph.getEdgeAtPosition ( int pos )

Definition at line 2649 of file DGraph.java.

References denoptim.graph.DGraph.gEdges.

Referenced by denoptim.graph.DGraph.getEdgesWithChild(), denoptim.graph.DGraph.getIndexOfEdgesWithChild(), denoptim.graph.AttachmentPointTest.testGetEmbeddedAP(), denoptim.fragspace.GraphLinkFinderTest.testLinkFromEdge(), denoptim.fragspace.GraphLinkFinderTest.testLinkFromEdgeNoMatch(), and denoptim.fragspace.GraphLinkFinderTest.testLinkFromEdgeOneMatch().

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◆ getEdgeCount()

int denoptim.graph.DGraph.getEdgeCount ( )

Definition at line 2658 of file DGraph.java.

References denoptim.graph.DGraph.gEdges.

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◆ getEdgeList()

List< Edge > denoptim.graph.DGraph.getEdgeList ( )

Definition at line 764 of file DGraph.java.

References denoptim.graph.DGraph.gEdges.

Referenced by denoptim.graph.DGraph.appendGraphOnAP(), denoptim.graph.DGraph.changeSignOfVertexID(), denoptim.gui.GraphViewerPanel.convertDnGraphToGSGraph(), denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getBondingAPIndex(), denoptim.graph.DGraph.getEdgesWithSrc(), denoptim.graph.DGraph.getEdgesWithTrg(), denoptim.utils.GraphConversionTool.getJGraphFromGraph(), denoptim.utils.GraphConversionTool.getJGraphKernelFromGraph(), and denoptim.graph.DGraph.getSourceVertex().

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◆ getEdgesWithChild()

ArrayList< Edge > denoptim.graph.DGraph.getEdgesWithChild ( int vid )

Parameters

vid

Returns: the edge whose source vertex is same as vid

Definition at line 3314 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeAtPosition(), denoptim.graph.DGraph.getEdgeCount(), and denoptim.graph.Edge.getSrcVertex().

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◆ getEdgesWithSrc()

List< Edge > denoptim.graph.DGraph.getEdgesWithSrc ( Vertex v )

Returns the list of edges that depart from the given vertex, i.e., edges where the srcAP is owned by the given vertex.

Parameters

v	the given vertex.

Returns: the list of edges departing from the given vertex.

Definition at line 784 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeList().

Referenced by denoptim.graph.DGraphTest.testGetEdgesWithSrcOrTrg().

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◆ getEdgesWithTrg()

List< Edge > denoptim.graph.DGraph.getEdgesWithTrg ( Vertex v )

Returns the list of edges that arrive from the given vertex, i.e., edges where the trgAP is owned by the given vertex.

Parameters

v	the given vertex.

Returns: the list of edges arriving to the given vertex.

Definition at line 805 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeList().

Referenced by denoptim.graph.DGraphTest.testGetEdgesWithSrcOrTrg().

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◆ getEdgeWithParent()

Edge denoptim.graph.DGraph.getEdgeWithParent ( long l )

Looks for an edge that points to a vertex with the given vertex id.

Parameters

l

Returns: the edge whose target vertex has ID same as vid, or null

Definition at line 3273 of file DGraph.java.

References denoptim.graph.Vertex.getEdgeToParent(), and denoptim.graph.DGraph.getVertexWithId().

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph().

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◆ getEmbeddedGraphInClone()

static DGraph denoptim.graph.DGraph.getEmbeddedGraphInClone	(	DGraph	graphY,
		DGraph	graphB,
		List< Template >	path
	)

static

Searches for a graphs (X) embedded at any level in a graph (Y) by knowing.

the embedding path (p) of another graph A that is embedded in graph B
and that graph Y is a unmodified clone of graph B, which implies that X is a clone of A.
Parameters

graphY where we want to find the analogous of graphA.

graphB the graph graphB where path points to graphA.

path the embedding path of graphA in graphB.

Returns
the graph embedded in graphY, i.e., graphX.

Definition at line 7085 of file DGraph.java.

References denoptim.graph.Template.getInnerGraph(), denoptim.graph.DGraph.getVertexAtPosition(), and denoptim.graph.DGraph.indexOf().

Referenced by denoptim.ga.XoverSite.projectToClonedGraphs(), and denoptim.graph.DGraphTest.testGetEmbeddedGraphInClone().

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◆ getEmbeddingPath()

List< Template > denoptim.graph.DGraph.getEmbeddingPath ( )

Find the path that one has to traverse to reach this graph from any template-embedding structure.

In practice, for a graph that is embedded a template jacket T1, which is part of another graph which is itself embedded in a template T2, which is again part of another graph, and so on it returns the references to the embedding templates stating from the outermost to the template that embeds this graph (Outermost reference come first in the resulting list). Instead a graph that is not embedded returns an empty path.

Returns: the path of references that allow to reach this graph from the outermost level of embedding.

Definition at line 6965 of file DGraph.java.

References denoptim.graph.DGraph.getEmbeddingPath(), denoptim.graph.Vertex.getGraphOwner(), and denoptim.graph.DGraph.templateJacket.

Referenced by denoptim.graph.DGraph.getEmbeddingPath(), denoptim.ga.XoverSite.projectToClonedGraphs(), denoptim.graph.DGraphTest.testGetEmbeddedGraphInClone(), and denoptim.graph.DGraphTest.testGetEmbeddingPath().

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◆ getFreeRCVertices()

ArrayList< Vertex > denoptim.graph.DGraph.getFreeRCVertices ( )

Search for unused ring closing vertices: vertices that contain only a RingClosingAttractor and are not part of any DENOPTIMRing

Returns: the list of unused ring closing vertices

Definition at line 984 of file DGraph.java.

References denoptim.graph.DGraph.getRCVertices(), and denoptim.graph.DGraph.isVertexInRing().

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.graph.DGraph.getUsedRCVertices(), and denoptim.graph.rings.RingSizeManager.initialize().

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◆ getGraphId()

int denoptim.graph.DGraph.getGraphId ( )

Definition at line 265 of file DGraph.java.

References denoptim.graph.DGraph.graphId.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.graph.DGraph.addVertex(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.graph.DGraph.editGraph(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.utils.GraphUtils.getLabel(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), denoptim.ga.EAUtils.outputPopulationDetails(), and denoptim.ga.GraphOperations.performMutation().

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◆ getHeavyAtomsCount()

int denoptim.graph.DGraph.getHeavyAtomsCount ( )

Calculate the number of atoms from the graph representation.

Returns: number of heavy atoms in the molecule

Definition at line 3953 of file DGraph.java.

References denoptim.graph.DGraph.getVertexList().

Referenced by denoptim.graph.Template.getHeavyAtomsCount(), and denoptim.ga.EAUtils.getMolSizeProbability().

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◆ getIndexOfEdgesWithChild()

ArrayList< Integer > denoptim.graph.DGraph.getIndexOfEdgesWithChild ( int vid )

Parameters

vid

Returns: the indices of all edges whose source vertex is same as vid

Definition at line 3291 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeAtPosition(), denoptim.graph.DGraph.getEdgeCount(), and denoptim.graph.Edge.getSrcVertex().

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◆ getInterfaceAPs()

List< AttachmentPoint > denoptim.graph.DGraph.getInterfaceAPs ( List< Vertex > subGraphB )

Searches for all AttachmentPoints that represent the interface between a subgraph, identified by the given list of vertices, and any other vertex, i.e., either belonging to the same graph but not to the same subgraph, or belonging to an outer embedding level.

Parameters

subGraphB list of vertices belonging to the subgraph.

Returns: the list of attachment points at the interface of the subgraph.

Definition at line 7113 of file DGraph.java.

Referenced by denoptim.fragspace.APMapFinder.APMapFinder(), denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.graph.DGraphTest.testGetInterfaceAPs(), and denoptim.ga.XoverSite.XoverSite().

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◆ getLevel()

int denoptim.graph.DGraph.getLevel ( Vertex v )

Calculates the level of a vertex in this graph.

Parameters

v	the vertex for which we want the level.

Returns: the level, i.e., an integer that is -1 for the seed vertex of this graph and increases by one unit per each edge that has to be traversed to reach the vertex given as argument via a direct path.

Definition at line 5326 of file DGraph.java.

References denoptim.graph.DGraph.getParentTree().

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.DGraph.findVertices(), denoptim.graph.DGraph.removeChainUpToBranching(), and denoptim.graph.DGraphTest.testGetLevel().

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◆ getLocalMsg()

String denoptim.graph.DGraph.getLocalMsg ( )

Definition at line 279 of file DGraph.java.

References denoptim.graph.DGraph.localMsg.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), and denoptim.ga.GraphOperations.performMutation().

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◆ getMaxVertexId()

long denoptim.graph.DGraph.getMaxVertexId ( )

Returns: the maximum value of vertex Id found in this graph.

Definition at line 3334 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.gui.GUIGraphHandler.extendCurrentGraph(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.DGraph.insertVertex(), denoptim.graph.DGraph.removeVertexAndWeld(), denoptim.graph.DGraph.replaceSubGraph(), denoptim.graph.DGraph.replaceVertex(), and denoptim.ga.EAUtils.setVertexCounterValue().

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◆ getMutableSites() [1/2]

List< Vertex > denoptim.graph.DGraph.getMutableSites ( )

A list of mutation sites from within this graph.

Returns: the list of vertices that allow any mutation type.

Definition at line 6622 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.ga.EAUtils.buildGraph(), and denoptim.graph.DGraphTest.testGetMutationSites().

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◆ getMutableSites() [2/2]

List< Vertex > denoptim.graph.DGraph.getMutableSites ( List< MutationType > ignoredTypes )

A list of mutation sites from within this graph.

Parameters

ignoredTypes a collection of mutation types to ignore. vertices that allow only ignored types of mutation will not be considered mutation sites.

Returns: the list of vertices that allow any non-ignored mutation type.

Definition at line 6642 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

◆ getOutermostGraphOwner()

DGraph denoptim.graph.DGraph.getOutermostGraphOwner ( )

Returns: the outermost graph object that can be reached from this possibly embedded graph.

Definition at line 6943 of file DGraph.java.

References denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.DGraph.getOutermostGraphOwner(), and denoptim.graph.DGraph.templateJacket.

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), and denoptim.graph.DGraph.getOutermostGraphOwner().

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◆ getParent()

Vertex denoptim.graph.DGraph.getParent ( Vertex v )

Definition at line 3168 of file DGraph.java.

References denoptim.graph.Vertex.getEdgeToParent(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.Edge.getSrcAP().

Referenced by denoptim.graph.DGraph.getParentTree().

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◆ getParentTree()

void denoptim.graph.DGraph.getParentTree	(	Vertex	vertex,
		List< Vertex >	parentTree
	)

Traverse the graph until it identifies the source of the directed path reachable from the given vertex recursively.

Parameters

vertex	the child vertex from which we start traversing the graph.
parentTree	list containing the references to all the parents recursively visited so far.

Definition at line 3149 of file DGraph.java.

References denoptim.graph.DGraph.getParent(), and denoptim.graph.DGraph.getParentTree().

Referenced by denoptim.graph.DGraph.getDeepestAmongThese(), denoptim.graph.DGraph.getLevel(), denoptim.graph.DGraph.getParentTree(), denoptim.graph.DGraph.getSourceVertex(), and denoptim.graph.rings.PathSubGraph.PathSubGraph().

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◆ getRCVertices()

ArrayList< Vertex > denoptim.graph.DGraph.getRCVertices ( )

Search for ring closing vertices: vertices that contain only a RingClosingAttractor

Returns: the list of ring closing vertices

Definition at line 962 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.graph.DGraph.getUsedRCVertices(), denoptim.graph.DGraph.replaceUnusedRCVsWithCapps(), denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability(), denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

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◆ getRingCount()

int denoptim.graph.DGraph.getRingCount ( )

Definition at line 2665 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

Referenced by denoptim.graph.DGraph.sameAs(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.graph.TemplateTest.testClone(), denoptim.graph.DGraphTest.testEmbedPatternsInTemplates(), denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem(), denoptim.graph.DGraphTest.testExtractSubgraph(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_Symmetry(), denoptim.graph.DGraphTest.testRemoveVertex(), denoptim.graph.DGraphTest.testReplaceSubGraph(), and denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

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◆ getRings()

List< Ring > denoptim.graph.DGraph.getRings ( )

Definition at line 771 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

Referenced by denoptim.graph.DGraph.appendGraphOnAP(), denoptim.gui.GraphViewerPanel.convertDnGraphToGSGraph(), denoptim.utils.GraphConversionTool.getJGraphFromGraph(), denoptim.utils.GraphConversionTool.getJGraphKernelFromGraph(), denoptim.graph.DGraph.sameAs(), denoptim.graph.TemplateTest.testClone(), denoptim.ga.GraphOperationsTest.testExtractPattern_returnsEmptyListIfNoRings(), and denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

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◆ getRingsInvolvingVertex() [1/2]

ArrayList< Ring > denoptim.graph.DGraph.getRingsInvolvingVertex ( Vertex v )

Returns the list of rings that include the given vertex in their fundamental cycle.

Parameters

v	the vertex to search for.

Returns: the list of rings of an empty list.

Definition at line 826 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.DGraph.removeVertex(), denoptim.graph.DGraph.replaceSingleSubGraph(), denoptim.graph.DGraph.replaceUnusedRCVsWithCapps(), and denoptim.graph.DGraph.sameAs().

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◆ getRingsInvolvingVertex() [2/2]

ArrayList< Ring > denoptim.graph.DGraph.getRingsInvolvingVertex ( Vertex[] vs )

Returns the list of rings that include the given list of vertices in their fundamental cycle.

Parameters

vs	the collection of vertices to search for.

Returns: the list of rings of an empty list.

Definition at line 847 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

◆ getRingsInvolvingVertexID()

ArrayList< Ring > denoptim.graph.DGraph.getRingsInvolvingVertexID ( int vid )

Definition at line 871 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

◆ getSourceVertex()

Vertex denoptim.graph.DGraph.getSourceVertex ( )

Identifies and return the vertex from which the spanning tree originates.

This is typically the first vertex in the list, but it is possible to programmatically build graphs that do not follow this convention. Therefore, here we test if the first vertex is a seed (i.e., it only has departing edges) and, if not, we search for the closest seed. WARNING: the graph is assumed to be an healthy spanning tree, in that it has only one seed that is reachable from any vertex by a inverse directed path. The result null for disconnected graphs or otherwise unhealthy spanning trees.

Returns: the seed/root of the spanning tree

Definition at line 740 of file DGraph.java.

References denoptim.graph.DGraph.getEdgeList(), denoptim.graph.DGraph.getParentTree(), denoptim.graph.DGraph.getVertexAtPosition(), and denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.DGraph.reorderVertexList(), denoptim.ga.GraphOperationsTest.testExtractPattern_singleRingSystem(), denoptim.graph.DGraphTest.testGetSourceVertex(), and denoptim.graph.DGraphTest.testReplaceSubGraph().

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◆ getSubgraphAPs()

List< AttachmentPoint > denoptim.graph.DGraph.getSubgraphAPs ( List< Vertex > subGraphB )

Searches for all AttachmentPoints that are owned by vertices in a subgraph but either available or used by vertices that do not belong to the subgraph.

Parameters

subGraphB list of vertices belonging to the subgraph.

Returns: the list of attachment points originating from the subgraph.

Definition at line 7148 of file DGraph.java.

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.ga.GraphOperations.performCrossover(), and denoptim.graph.DGraphTest.testGetSubgraphAPs().

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◆ getSymmetricSetCount()

int denoptim.graph.DGraph.getSymmetricSetCount ( )

Returns the number of symmetric sets of vertices.

Returns: the number of symmetric sets of vertices

Definition at line 313 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

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◆ getSymmetricSubGraphs()

List< List< Vertex > > denoptim.graph.DGraph.getSymmetricSubGraphs ( List< Vertex > subGrpVrtxs ) throws DENOPTIMException

We assume that the subgraph is a continuously connected, directed graph.

By contract, the source of the symmetric subgraph's spanning tree is always the first vertex in each returned list. Also, note that symmetry does not pertain capping groups, so capping groups are not expected to be among the vertices in the given list and will not be present in the resulting subgraphs.

Parameters

subGrpVrtxs

Returns: a collection of subgraphs, each represented by a list of vertices belonging to it.

Exceptions

DENOPTIMException if capping groups are present in the list.

Definition at line 1816 of file DGraph.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraph.getChildTreeLimited(), and denoptim.graph.DGraph.getSymVerticesForVertex().

Referenced by denoptim.graph.DGraph.replaceSubGraph(), and denoptim.graph.DGraphTest.testGetSymmetricSubGraphs().

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◆ getSymSetForVertex()

SymmetricVertexes denoptim.graph.DGraph.getSymSetForVertex ( Vertex v )

Returns the set of vertexes symmetric to the given one.

Parameters

v	the vertex for which we seek the symmetric vertexes.

Returns: either the collector of vertexes symmetric to the given one, which also includes the given one, or an empty collector.

Definition at line 633 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

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◆ getSymSetsIterator()

Iterator< SymmetricVertexes > denoptim.graph.DGraph.getSymSetsIterator ( )

Get an iterator for the sets of symmetrically related vertices.

Definition at line 324 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

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◆ getSymVerticesForVertex()

List< Vertex > denoptim.graph.DGraph.getSymVerticesForVertex ( Vertex v )

Parameters

v	the vertex for which we want the list of symmetric vertices.

Returns: a list that includes v but can be empty.

Definition at line 335 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.Template.getSymmetricAPSets(), denoptim.graph.DGraph.getSymmetricSubGraphs(), denoptim.graph.DGraph.insertVertex(), denoptim.graph.DGraph.removeVertexAndWeld(), denoptim.graph.DGraph.replaceVertex(), and denoptim.ga.GraphOperationsTest.testExtendGraph().

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◆ getTemplateJacket()

Template denoptim.graph.DGraph.getTemplateJacket ( )

Returns: the template that contains this graph or null.

Definition at line 6932 of file DGraph.java.

References denoptim.graph.DGraph.templateJacket.

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), and denoptim.ga.GraphOperations.performMutation().

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◆ getUniqueAPIndex()

int denoptim.graph.DGraph.getUniqueAPIndex ( )

protected

Definition at line 4051 of file DGraph.java.

References denoptim.graph.DGraph.apCounter.

Referenced by denoptim.graph.Vertex.getUniqueAPIndex().

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◆ getUsedRCVertices()

ArrayList< Vertex > denoptim.graph.DGraph.getUsedRCVertices ( )

Search for used ring closing vertices: vertices that contain only a RingClosingAttractor and are part of a DENOPTIMRing.

Returns: the list of ring closing vertices

Definition at line 1007 of file DGraph.java.

References denoptim.graph.DGraph.getFreeRCVertices(), and denoptim.graph.DGraph.getRCVertices().

Referenced by denoptim.ga.EAUtils.getCrowdedness().

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◆ getVertexAtPosition()

Vertex denoptim.graph.DGraph.getVertexAtPosition ( int pos )

Returns the vertex that is in the given position of the list of vertices belonging to this graph.

Parameters

pos	the position in the list.

Returns: the vertex in the given position.

Definition at line 2514 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

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◆ getVertexCount()

int denoptim.graph.DGraph.getVertexCount ( )

Definition at line 2672 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

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◆ getVertexList()

List< Vertex > denoptim.graph.DGraph.getVertexList ( )

Definition at line 719 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

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◆ getVertexWithId()

Vertex denoptim.graph.DGraph.getVertexWithId ( long vid )

Searches for a vertex with the given identifier.

Parameters

vid	the identifier

Returns: the first vertex found with such identifier, or null if no such identifier is found.

Definition at line 2582 of file DGraph.java.

References denoptim.graph.DGraph.gVertices, and denoptim.graph.DGraph.indexOfVertexWithID().

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◆ graphNeedsCappingGroups()

boolean denoptim.graph.DGraph.graphNeedsCappingGroups ( FragmentSpace fragSpace )

Checks the graph for unused APs that need to be capped.

Returns: true if the graph has at least one AP that needs to be capped

Definition at line 4064 of file DGraph.java.

References denoptim.fragspace.FragmentSpace.getAPClassOfCappingVertex(), and denoptim.graph.DGraph.getVertexList().

Referenced by denoptim.combinatorial.GraphBuildingTask.call().

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◆ hasForbiddenEnd()

boolean denoptim.graph.DGraph.hasForbiddenEnd ( FragmentSpaceParameters fsSettings )

Check if there are forbidden ends: free attachment points that are not suitable for capping and not allowed to stay unused.

Returns: true if a forbidden end is found

Definition at line 5686 of file DGraph.java.

References denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.graph.DGraph.getVertexList(), and denoptim.graph.APClass.toString().

Referenced by denoptim.graph.DGraph.checkConsistency().

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◆ hasOrEmbedsRings()

boolean denoptim.graph.DGraph.hasOrEmbedsRings ( )

Check for rings in this graph and in any graph that is embedded at any level in any vertex of this graph.

Does not consider any graph that embeds this graph.

Returns: true if there are rings in this graph or in embedded graphs.

Definition at line 906 of file DGraph.java.

References denoptim.graph.Template.getInnerGraph(), denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, and denoptim.graph.DGraph.hasOrEmbedsRings().

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.molecularmodeling.ChemicalObjectModel.ChemicalObjectModel(), and denoptim.graph.DGraph.hasOrEmbedsRings().

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◆ hasRings()

boolean denoptim.graph.DGraph.hasRings ( )

Check for rings in this graph.

Does not cross the template-barrier, i.e., ignores any ring that is embedded at any level in any vertex of this graph, neither in any graph that embeds this graph.

Returns: true if there are rings in this graph.

Definition at line 892 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

◆ hasScaffoldTypeVertex()

boolean denoptim.graph.DGraph.hasScaffoldTypeVertex ( )

Checks if this graph contains a scaffold vertex.

Returns: true if there is a scaffold vertex.

Definition at line 6909 of file DGraph.java.

References denoptim.graph.DGraph.getVertexList(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.graph.DGraph.embedPatternsInTemplates().

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◆ hasSymmetricAP()

boolean denoptim.graph.DGraph.hasSymmetricAP ( )

Definition at line 286 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

Referenced by denoptim.fragspace.FragsCombinationIterator.next().

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◆ hasSymmetryInvolvingVertex()

boolean denoptim.graph.DGraph.hasSymmetryInvolvingVertex ( Vertex v )

Definition at line 293 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.DGraph.convertSymmetricLabelsToSymmetricSets(), denoptim.ga.GraphOperations.deleteChain(), denoptim.ga.GraphOperations.deleteFragment(), denoptim.ga.GraphOperations.extendGraph(), denoptim.ga.GraphOperations.rebuildBranch(), and denoptim.graph.DGraph.removeBranchStartingAt().

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◆ indexOf()

int denoptim.graph.DGraph.indexOf ( Vertex v )

Returns the index of a vertex in the list of vertices of this graph.

Parameters

v	the vertex to search

Returns: the index of the vertex in the list of vertices.

Definition at line 2569 of file DGraph.java.

References denoptim.graph.DGraph.gVertices.

Referenced by denoptim.ga.GraphOperations.addRing(), denoptim.graph.DGraph.extractSubgraph(), denoptim.graph.DGraph.getEmbeddedGraphInClone(), denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.ga.GraphOperations.performMutation(), and denoptim.ga.GraphOperationsTest.testLocateCompatibleXOverPoints().

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◆ indexOfVertexWithID()

int denoptim.graph.DGraph.indexOfVertexWithID ( long vid )

Returns the position of the first vertex that has the given ID.

Parameters

vid	the vertedID of the vertex we are looking for.

Returns: the index in the list of vertices.

Definition at line 2598 of file DGraph.java.

References denoptim.graph.Vertex.getVertexId(), and denoptim.graph.DGraph.gVertices.

Referenced by denoptim.graph.DGraph.getVertexWithId().

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◆ insertSingleVertex()

boolean denoptim.graph.DGraph.insertSingleVertex	(	Edge	edge,
		Vertex	newLink,
		LinkedHashMap< AttachmentPoint, AttachmentPoint >	apMap
	)		throws DENOPTIMException

Inserts a given vertex in between two vertices connected by the given edge.

This method reproduces the change of vertex on all symmetric sites.

Parameters

edge	the edge where to insert the new vertex.
newLink	the new vertex to be inserted.
apMap	the mapping of attachment points needed to install the new vertex and connect it to the rest of the graph. The syntax of this map must be: keys: the APs originally involved in making the edge given as parameter, values: the APs in the new vertex.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException

Definition at line 2440 of file DGraph.java.

Referenced by denoptim.graph.DGraph.insertVertex().

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◆ insertVertex()

boolean denoptim.graph.DGraph.insertVertex	(	Edge	edge,
		int	bbId,
		BBType	bbt,
		LinkedHashMap< AttachmentPoint, Integer >	apMap,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Inserts a given vertex in between two vertices connected by the given edge.

This method reproduces the change of vertex on all symmetric sites.

Parameters

edge	the edge where to insert the new vertex.
bbId	the building block Id of the building blocks that will be inserted.
bbt	the type of building block to be inserted.
apMap	the mapping of attachment points needed to install the new building block and connect it to the rest of the graph. The syntax of this map must be: keys: the APs originally involved in making the edge given as parameter, values: the 0-based index of the AP in the new building block that will be inserted.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException

Definition at line 2360 of file DGraph.java.

References denoptim.graph.SymmetricSet< T >.add(), denoptim.graph.DGraph.addSymmetricSetOfVertices(), denoptim.utils.GraphUtils.ensureVertexIDConsistency(), denoptim.graph.DGraph.gEdges, denoptim.graph.Vertex.getAP(), denoptim.graph.DGraph.getMaxVertexId(), denoptim.graph.Edge.getSrcAP(), denoptim.graph.DGraph.getSymVerticesForVertex(), denoptim.graph.Edge.getTrgAP(), denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.DGraph.insertSingleVertex(), and denoptim.graph.Vertex.newVertexFromLibrary().

Referenced by denoptim.ga.GraphOperations.extendLink().

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◆ isIsomorphicTo()

boolean denoptim.graph.DGraph.isIsomorphicTo ( DGraph other )

Checks if this graph is "DENOPTIM-isomorphic" to the other one given.

"DENOPTIM-isomorphic" is a DENOPTIM-specific definition of
graph isomorphism that differs from the most common meaning of isomorphism in graph theory. In general, graph are considered undirected when evaluating DENOPTIM-isomorphism. Next, since a graph is effectively a spanning tree (ST_i={{vertices}, {acyclic edges}}) with a set of fundamental cycles (FC_i={C_1, C_2,...C_n}), any graph G={ST_i,FC_i} that contains one or more cycles can be represented in multiple ways, G={ST_j,FC_j} or G={ST_k,FC_k}, that differ by the position of the chord/s and by the corresponding pair of ring-closing vertices between which each chord is defined. The DENOPTIM-isomorphism for two graph G1 and G2 is given by the common graph theory isomorphism between two undirected graphs U1 and U2 build respectively from G1 and G2 with the convention defined in GraphConversionTool#getJGraphFromGraph(DGraph). Finally,

vertices are compared excluding their vertex ID, i.e., Vertex#sameAs()
edges are considered undirected and compared considering the BondType and the identity of the attachment points connected thereby. This latter point has an important implication: two apparently equal graphs (same vertices that are connected to each other forming the same vertex-chains) can be non-isomorphic when the APs used to connect two vertices are not the same. Chemically, this means the stereochemistry around one or both vertices, is different in the two graphs. Therefore two otherwise equal-looking graphs can very well be, de facto, not isomorphic.

This method makes use of the Vento-Foggia VF2 algorithm (see DOI:10.1109/TPAMI.2004.75) as provided by JGraphT library in VF2GraphIsomorphismInspector.

Detection of isomorphism can be very slow for pathological cases and for graphs with large symmetric systems! TODO: consider adding a runtime limit or a further simplification/speed-up exploiting symmetry. The symmetry, however, does not help detecting isomorphism between a graph with symmetric branches and its isomorphic analog that is fully asymmetric.

Parameters

other the graph to be compared with this.

Returns: true is this graph is isomorphic to the other.

Definition at line 3453 of file DGraph.java.

References denoptim.graph.simplified.UndirectedEdge.compare(), denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.Vertex.getGraphOwner(), denoptim.utils.GraphConversionTool.getJGraphFromGraph(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.jGraph, and denoptim.graph.Vertex.sameAs().

Referenced by denoptim.ga.GraphOperations.locateCompatibleXOverPoints(), denoptim.ga.GraphOperations.processPermutationOfEndPoints(), denoptim.programs.graphlisthandler.GraphListsHandler.runProgram(), denoptim.programs.isomorphism.Isomorphism.runProgram(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), denoptim.graph.DGraphTest.testExtractSubgraph(), denoptim.graph.DGraphTest.testGraphIsomorphism(), denoptim.graph.DGraphTest.testIsIsostructuralTo(), denoptim.graph.DGraphTest.testReplaceSubGraph(), and denoptim.graph.DGraphTest.testReplaceVertex_inRing().

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◆ isIsostructuralTo()

boolean denoptim.graph.DGraph.isIsostructuralTo ( DGraph other )

Checks if this graph is "DENOPTIM-isostructural" to the other one given.

"DENOPTIM-isostructural" means that the two graphs are isomorfic when:

the comparison of the vertices considers any implementation of Vertex equals to itself unless two vertices differ by the return value of Vertex#isRCV(),
the comparison of the vertices considers only the type of bond the edge corresponds to (if any),
free AttachmentPoints that are marked as required in either graph are reflected in the other.

Parameters

other

Returns

Definition at line 3580 of file DGraph.java.

References denoptim.graph.simplified.Node.compare(), denoptim.graph.simplified.NodeConnection.compare(), denoptim.graph.simplified.Node.getDNPVertex(), denoptim.graph.Vertex.getGraphOwner(), denoptim.utils.GraphConversionTool.getJGraphKernelFromGraph(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.jGraphKernel, and denoptim.graph.simplified.Node.REFTOVERTEXKERNEL.

Referenced by denoptim.ga.GraphOperations.checkAndAddXoverSites(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), and denoptim.graph.DGraphTest.testIsIsostructuralTo().

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◆ isReversible()

boolean denoptim.graph.DGraph.isReversible ( FragmentSpace fragSpace )

Checks is the every edge in the graph can be defined in the opposite direction according to the APClass compatibility rules.

Note that the reversions operation on a branched subgraph generates a graph with multiple source vertices, which is not allowed. Yet, the reversion is formally possible.

Returns: true if the all edges can be reverted and retain consistency with APClass compatibility rules.

Definition at line 7054 of file DGraph.java.

References denoptim.graph.DGraph.gEdges.

◆ isVertexIDInRing()

boolean denoptim.graph.DGraph.isVertexIDInRing ( int vid )

Definition at line 924 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

◆ isVertexInRing()

boolean denoptim.graph.DGraph.isVertexInRing ( Vertex v )

Definition at line 940 of file DGraph.java.

References denoptim.graph.DGraph.gRings.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.utils.GraphConversionTool.getJGraphFromGraph(), denoptim.utils.GraphConversionTool.getJGraphKernelFromGraph(), denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.DGraph.removeCappingGroups(), denoptim.graph.DGraph.removeCappingGroupsOn(), and denoptim.graph.DGraph.removeVertex().

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◆ makeAllGraphsWithDifferentRingSets()

ArrayList< DGraph > denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets ( RunTimeParameters settings ) throws DENOPTIMException

Evaluates the possibility of closing rings in this graph and generates all alternative graphs resulting by different combinations of rings.

Returns: true unless no ring can be set up even if required

Exceptions

denoptim.exception.DENOPTIMException

Definition at line 5589 of file DGraph.java.

References denoptim.graph.DGraph.addRing(), denoptim.graph.Ring.addVertex(), denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.graph.rings.RingClosureParameters.buildChelatesMode, denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.graph.DGraph.clone(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), denoptim.fragspace.FragmentSpaceParameters.getRotSpaceDefFile(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.graph.DGraph.getVertexWithId(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.DGraph.renumberVerticesGetMap(), denoptim.molecularmodeling.ThreeDimTreeBuilder.setAlignBBsIn3D(), denoptim.graph.Ring.setBondType(), denoptim.graph.DGraph.setGraphId(), denoptim.graph.DGraph.setRings(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

Referenced by denoptim.combinatorial.GraphBuildingTask.call().

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◆ reassignSymmetricLabels()

void denoptim.graph.DGraph.reassignSymmetricLabels ( )

protected

Marks the vertices of this graph with a string that is consistent for all vertices that belong to symmetric sets.

All vertices will get a label, whether they belong to a symmetric set or not. The label is places in the vertex property DENOPTIMConstants#VRTSYMMSETID. Any previous labeling is ignored and overwritten.

Definition at line 1568 of file DGraph.java.

References denoptim.graph.DGraph.getSymSetsIterator(), denoptim.graph.DGraph.gVertices, and denoptim.constants.DENOPTIMConstants.VRTSYMMSETID.

Referenced by denoptim.graph.DGraph.replaceVertex(), denoptim.graph.DGraphTest.testReplaceSubGraph(), and denoptim.graph.DGraphTest.testSymmetricSetLabels().

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◆ removeBranchStartingAt() [1/2]

boolean denoptim.graph.DGraph.removeBranchStartingAt ( Vertex v ) throws DENOPTIMException

Deletes the branch, i.e., the specified vertex and its children.

Updates symmetry accordingly, but does not remove symmetric branches.

Parameters

vid	the vertexID of the root of the branch. We'll remove also this vertex.

Returns: true if operation is successful

Exceptions

DENOPTIMException

Definition at line 4821 of file DGraph.java.

References denoptim.graph.DGraph.removeEdge(), and denoptim.graph.DGraph.removeOrphanBranchStartingAt().

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◆ removeBranchStartingAt() [2/2]

boolean denoptim.graph.DGraph.removeBranchStartingAt	(	Vertex	v,
		boolean	symmetry
	)		throws DENOPTIMException

Deletes the branch, i.e., the specified vertex and its children.

Parameters

vid	the vertexID of the root of the branch. We'll remove also this vertex.
symmetry	use `true` to enforce deletion of all symmetric vertices.

Returns: true if operation is successful.

Exceptions

DENOPTIMException

Definition at line 4788 of file DGraph.java.

References denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.hasSymmetryInvolvingVertex(), and denoptim.graph.DGraph.removeBranchStartingAt().

Referenced by denoptim.ga.GraphOperations.deleteFragment(), denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.removeBranchStartingAt(), and denoptim.graph.Template.removeProjectionOfInnerAP().

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◆ removeCappingGroups() [1/2]

void denoptim.graph.DGraph.removeCappingGroups ( )

Remove all capping groups on this graph.

Definition at line 4156 of file DGraph.java.

References denoptim.graph.DGraph.gVertices, and denoptim.graph.DGraph.removeCappingGroups().

Referenced by denoptim.graph.DGraph.removeCappingGroups(), and denoptim.graph.DGraph.removeCappingGroupsFromChilds().

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◆ removeCappingGroups() [2/2]

void denoptim.graph.DGraph.removeCappingGroups ( List< Vertex > lstVerts )

Remove capping groups that belong to this graph and are in the given list.

Parameters

lstVerts the list of vertices to analyze.

Definition at line 4114 of file DGraph.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.getVertexWithId(), denoptim.graph.DGraph.isVertexInRing(), and denoptim.graph.DGraph.removeVertex().

Referenced by denoptim.graph.DGraphTest.testRemoveCapping().

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◆ removeCappingGroupsFromChilds()

void denoptim.graph.DGraph.removeCappingGroupsFromChilds ( List< Vertex > lstVerts )

Definition at line 4142 of file DGraph.java.

References denoptim.graph.DGraph.getChildVertices(), and denoptim.graph.DGraph.removeCappingGroups().

Referenced by denoptim.graph.DGraph.replaceSubGraph().

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◆ removeCappingGroupsOn()

void denoptim.graph.DGraph.removeCappingGroupsOn ( Vertex vertex )

Remove capping groups on the given vertex of this graph.

Definition at line 4084 of file DGraph.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraph.getChildVertices(), denoptim.graph.DGraph.isVertexInRing(), and denoptim.graph.DGraph.removeVertex().

Referenced by denoptim.graph.DGraphTest.testRemoveCapping().

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◆ removeChainUpToBranching()

boolean denoptim.graph.DGraph.removeChainUpToBranching	(	Vertex	v,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Mutates the graph by removing the chain where a given vertex is located up to the first branching (i.e., to non-capping group) on either side.

The graph is updated accordingly. In particular, the direction of edges in the surviving graph and the definition of fundamental cycles are changed to reflect the change of spanning tree.

Parameters

v	the vertex from which we start detecting a chain

Returns: true if successful.

Exceptions

DENOPTIMException is any assumption on the healthy structure of this graph is not verified.

Definition at line 4878 of file DGraph.java.

Referenced by denoptim.ga.GraphOperations.deleteChain().

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◆ removeEdge()

void denoptim.graph.DGraph.removeEdge ( Edge edge )

Removes an edge and update the free valences of the attachment points that were originally involved in this edge.

Parameters

edge

Definition at line 2620 of file DGraph.java.

References denoptim.graph.DGraph.gEdges, denoptim.graph.Edge.getSrcAP(), denoptim.graph.Edge.getTrgAP(), denoptim.graph.DGraph.jGraph, denoptim.graph.DGraph.jGraphKernel, and denoptim.graph.AttachmentPoint.setUser().

Referenced by denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.DGraph.removeBranchStartingAt(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.DGraph.removeVertex(), denoptim.graph.DGraph.replaceSingleSubGraph(), and denoptim.graph.EdgeTest.testConnectionDeconnectionLoop().

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◆ removeOrphanBranchStartingAt()

boolean denoptim.graph.DGraph.removeOrphanBranchStartingAt ( Vertex v ) throws DENOPTIMException

Deletes the branch, i.e., the specified vertex and its children.

This method does not cross template boundaries, thus all children belong to the same graph. Symmetry relations are updated accordingly.

Parameters

vid	the vertexID of the root of the branch. We'll remove also this vertex.
allowOrphan	use `true` to allow removal of branches starting with a vertex that has no edge to a parent.

Returns: true if operation is successful

Exceptions

DENOPTIMException

Definition at line 4847 of file DGraph.java.

References denoptim.graph.DGraph.getChildrenTree(), denoptim.graph.DGraph.getVertexWithId(), and denoptim.graph.DGraph.removeVertex().

Referenced by denoptim.graph.DGraph.removeBranchStartingAt(), and denoptim.graph.DGraph.removeSingleVertexAndWeld().

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◆ removeRing()

void denoptim.graph.DGraph.removeRing ( Ring ring )

Definition at line 2637 of file DGraph.java.

References denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

Referenced by denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), denoptim.graph.DGraph.removeVertex(), and denoptim.ga.GraphOperationsTest.testExtractPattern_returnsEmptyListIfNoRings().

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◆ removeSingleVertexAndWeld()

boolean denoptim.graph.DGraph.removeSingleVertexAndWeld	(	Vertex	vertex,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Remove a given vertex belonging to this graph and re-connects the resulting graph branches as much as possible.

Parameters

vertex the vertex currently belonging to this graph and to be replaced.

Returns: true if the operation is successful.

Exceptions

DENOPTIMException

Definition at line 1247 of file DGraph.java.

Referenced by denoptim.graph.DGraph.removeSingleVertexAndWeld(), and denoptim.graph.DGraph.removeVertexAndWeld().

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◆ removeSymmetryRedundance()

void denoptim.graph.DGraph.removeSymmetryRedundance ( List< Vertex > list )

Remove all but one of the symmetry-related partners in a list of vertices.

The vertices must belong to this graph.

Parameters

list	vertices to be purged.

Definition at line 6392 of file DGraph.java.

References denoptim.graph.DGraph.getSymSetsIterator().

Referenced by denoptim.graph.DGraph.findVertices(), and denoptim.graph.DGraph.removeSymmetryRedundantIds().

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◆ removeSymmetryRedundantIds()

void denoptim.graph.DGraph.removeSymmetryRedundantIds ( ArrayList< Long > list )

Remove all but one of the symmetry-related partners in a given list of vertex IDs.

The vertices must belong to this graph.

Parameters

list	the list of vertex IDs to be purged.

Definition at line 6426 of file DGraph.java.

References denoptim.graph.DGraph.getVertexWithId(), and denoptim.graph.DGraph.removeSymmetryRedundance().

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◆ removeSymmetrySet()

void denoptim.graph.DGraph.removeSymmetrySet ( SymmetricVertexes ss )

Removed the given symmetric set, if present.

Parameters

ss	the symmetric relation to be removed.

Definition at line 620 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.DGraph.removeChainUpToBranching().

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◆ removeVertex()

void denoptim.graph.DGraph.removeVertex ( Vertex vertex )

Remove a vertex from this graph.

This method removes also edges and rings that involve the given vertex. Symmetric sets of vertices are corrected accordingly: they are removed if there is only one remaining vertex in the set, or purged from the vertex being removed.

Parameters

vertex the vertex to remove.

Definition at line 1119 of file DGraph.java.

References denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.getRingsInvolvingVertex(), denoptim.graph.Edge.getSrcVertex(), denoptim.graph.Edge.getTrgVertex(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.isVertexInRing(), denoptim.graph.DGraph.jGraph, denoptim.graph.DGraph.jGraphKernel, denoptim.graph.DGraph.removeEdge(), denoptim.graph.DGraph.removeRing(), denoptim.graph.Vertex.resetGraphOwner(), and denoptim.graph.DGraph.symVertices.

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◆ removeVertexAndWeld()

boolean denoptim.graph.DGraph.removeVertexAndWeld	(	Vertex	vertex,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Remove a given vertex belonging to this graph and re-connects the resulting graph branches as much as possible.

This method reproduces the change of vertex on all symmetric sites.

Parameters

oldLink the vertex currently belonging to this graph and to be replaced.

Returns: true if the operation is successful.

Exceptions

DENOPTIMException

Definition at line 1195 of file DGraph.java.

References denoptim.utils.GraphUtils.ensureVertexIDConsistency(), denoptim.graph.DGraph.getMaxVertexId(), denoptim.graph.DGraph.getSymVerticesForVertex(), denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, denoptim.graph.AttachmentPoint.hasConnectedSrcAtom(), denoptim.graph.AttachmentPoint.hasSameSrcAtom(), and denoptim.graph.DGraph.removeSingleVertexAndWeld().

Referenced by denoptim.ga.GraphOperations.deleteLink().

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◆ renumberGraphVertices()

void denoptim.graph.DGraph.renumberGraphVertices ( )

Reassign vertex IDs to all vertices of this graph.

The old IDs are stored in the vertex property DENOPTIMConstants#STOREDVID.

Definition at line 5283 of file DGraph.java.

References denoptim.graph.DGraph.renumberVerticesGetMap().

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◆ renumberVerticesGetMap()

Map< Long, Long > denoptim.graph.DGraph.renumberVerticesGetMap ( )

Reassign vertex IDs to a graph.

The old IDs are stored in the vertex property DENOPTIMConstants#STOREDVID.

Returns: map with old IDs as key and new IDs as values.

Definition at line 5296 of file DGraph.java.

References denoptim.utils.GraphUtils.getUniqueVertexIndex(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.getVertexList(), denoptim.graph.Vertex.setProperty(), denoptim.graph.Vertex.setVertexId(), and denoptim.constants.DENOPTIMConstants.STOREDVID.

Referenced by denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), and denoptim.graph.DGraph.renumberGraphVertices().

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◆ reorderVertexList()

static void denoptim.graph.DGraph.reorderVertexList ( DGraph g )

staticprivate

Sets the vertex at the lowest level as the scaffold, changes the
directions of edges so that the scaffold is the source, and changes the levels of the graph's other vertices to be consistent with the new scaffold.

Parameters

g	Graph to fix.

Definition at line 4717 of file DGraph.java.

References denoptim.graph.DGraph.fixEdgeDirections(), denoptim.graph.DGraph.getSourceVertex(), and denoptim.graph.DGraph.setScaffold().

Referenced by denoptim.graph.DGraph.extractPattern().

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◆ replaceSingleSubGraph()

boolean denoptim.graph.DGraph.replaceSingleSubGraph	(	List< Vertex >	subGrpVrtxs,
		DGraph	newSubGraph,
		LinkedHashMap< AttachmentPoint, AttachmentPoint >	apMap
	)		throws DENOPTIMException

Replaced the subgraph represented by a given collection of vertices that belong to this graph.

This method does not project the change of vertex on symmetric sites, and does not alter the symmetric sets. To properly manage symmetry, you should run DGraph#reassignSymmetricLabels() on newSubGraph prior to calling this method, and, after running this method, call DGraph#convertSymmetricLabelsToSymmetricSets() on this graph. This strategy reflects the fact that multiple sub-graph replacements can introduce vertices that are symmetric throughout these newly inserted subgraphs, thus a single subgraph replacement cannot know the complete list of symmetric vertices. Therefore, the handling of the symmetry is left outside of the subgraph replacement operation.

Parameters

subGrpVrtxs	the vertices currently belonging to this graph and to be replaced. We assume these collection of vertices is a connected subgraph, i.e., all vertices are reachable by one single vertex via a directed path that does not involve any other vertex not included in this collections.
newSubGraph	the graph that will be attached on this graph. No copying or cloning: such graph contains the actual vertices that will become part of this graph.
apMap	mapping of attachment points belonging to any vertex in `subGrpVrtxs` to attachment points in `newSubGraph`.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException

Definition at line 1954 of file DGraph.java.

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.replaceSubGraph(), denoptim.graph.DGraph.replaceVertex(), denoptim.graph.DGraphTest.testIsIsostructuralTo(), denoptim.graph.DGraphTest.testReplaceSubGraph(), and denoptim.graph.DGraphTest.testReplaceSubGraph_inTemplate().

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◆ replaceSubGraph()

boolean denoptim.graph.DGraph.replaceSubGraph	(	List< Vertex >	subGrpVrtxs,
		DGraph	incomingGraph,
		LinkedHashMap< AttachmentPoint, AttachmentPoint >	apMap,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Replaced the subgraph represented by a given collection of vertices that belong to this graph.

This method reproduces the change of vertex on all symmetric sites, where a site is identified by a symmetrically identified reflection of the subgraph to replace, which are identified using symmetric sets.

Parameters

subGrpVrtxs	the vertices currently belonging to this graph and to be replaced. We assume these collection of vertices is a connected graph, i.e., all vertices are reachable by one single vertex via a directed path that does not involve any other vertex not included in this collections.
newSubGraph	the graph that will be used to create the new branch replacing the old one. Vertices of such branch will be cloned to create the new vertices to be added to this graph.
apMap	mapping of attachment points belonging to any vertex in `subGrpVrtxs` to attachment points in `newSubGraph`.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException is capping groups are the only vertices in the subgraph.

Definition at line 1680 of file DGraph.java.

Referenced by denoptim.graph.DGraph.embedPatternsInTemplates(), and denoptim.ga.GraphOperations.performCrossover().

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◆ replaceUnusedRCVsWithCapps()

void denoptim.graph.DGraph.replaceUnusedRCVsWithCapps ( FragmentSpace fragSpace ) throws DENOPTIMException

Removes unused ring-closing vertices.

If the resulting free AP needs to be capped, then the proper capping group is places where a ring-closing vertex once stood.

Parameters

fragSpace the fragment space defining how capping is configured.

Exceptions

DENOPTIMException

Definition at line 1526 of file DGraph.java.

References denoptim.graph.DGraph.appendVertexOnAP(), denoptim.graph.Vertex.getAP(), denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.DGraph.getRCVertices(), denoptim.graph.DGraph.getRingsInvolvingVertex(), denoptim.graph.Vertex.getVertexId(), denoptim.graph.DGraph.removeVertex(), and denoptim.graph.Vertex.setVertexId().

Referenced by denoptim.combinatorial.GraphBuildingTask.call(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), and denoptim.graph.DGraphTest.testRemoveUnusedRCVs().

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◆ replaceVertex() [1/2]

boolean denoptim.graph.DGraph.replaceVertex	(	Vertex	vertex,
		int	bbId,
		BBType	bbt,
		LinkedHashMap< Integer, Integer >	apIdMap,
		boolean	symmetry,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Replaced a given vertex belonging to this graph with a new vertex generated specifically for this purpose.

Parameters

vertex	the vertex currently belonging to this graph and to be replaced.
bbId	the building block Id of the building blocks that will replace the original vertex.
bbt	the type of building block to be used to replace the original vertex.
apMap	the mapping of attachment points needed to install the new vertex in the slot of the old one and recreate the edges to the rest of the graph.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException

Definition at line 2282 of file DGraph.java.

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◆ replaceVertex() [2/2]

boolean denoptim.graph.DGraph.replaceVertex	(	Vertex	vertex,
		int	bbId,
		BBType	bbt,
		LinkedHashMap< Integer, Integer >	apIdMap,
		FragmentSpace	fragSpace
	)		throws DENOPTIMException

Replaced a given vertex belonging to this graph with a new vertex generated specifically for this purpose.

This method reproduces the change of vertex on all symmetric sites.

Parameters

vertex	the vertex currently belonging to this graph and to be replaced.
bbId	the building block Id of the building blocks that will replace the original vertex.
bbt	the type of building block to be used to replace the original vertex.
apMap	the mapping of attachment points needed to install the new vertex in the slot of the old one and recreate the edges to the rest of the graph.

Returns: true if the substitution is successful.

Exceptions

DENOPTIMException

Definition at line 2258 of file DGraph.java.

References denoptim.graph.DGraph.replaceVertex().

Referenced by denoptim.graph.DGraph.editGraph(), denoptim.graph.DGraph.replaceVertex(), denoptim.ga.GraphOperations.substituteLink(), denoptim.graph.DGraphTest.testReplaceVertex(), and denoptim.graph.DGraphTest.testReplaceVertex_inRing().

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◆ sameAs()

boolean denoptim.graph.DGraph.sameAs	(	DGraph	other,
		StringBuilder	reason
	)

Compare this and another graph ignoring the vertex IDs.

This method looks into the structure of the graphs to determine if the two graphs have the same spanning tree, same symmetric sets, and same rings set, despite having different vertex IDs. Does not check for alternative permutations nor alternatives spanning trees so it returns false for isomorphic graphs that are represented by different spanning trees.

Parameters

other the other graph to be compared with this graph

Returns: true if the two graphs represent the same system

Definition at line 3665 of file DGraph.java.

References denoptim.graph.DGraph.compareGraphNodes(), denoptim.graph.DGraph.getEdgeCount(), denoptim.graph.DGraph.getRingCount(), denoptim.graph.DGraph.getRings(), denoptim.graph.DGraph.getRingsInvolvingVertex(), denoptim.graph.DGraph.getSymmetricSetCount(), denoptim.graph.DGraph.getSymSetForVertex(), denoptim.graph.DGraph.getSymSetsIterator(), denoptim.graph.DGraph.getVertexAtPosition(), denoptim.graph.DGraph.getVertexCount(), and denoptim.graph.DGraph.sameAsRings().

Referenced by denoptim.ga.Population.getXoverPartners(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_Free(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FreeBackwards(), denoptim.graph.DGraphTest.testSameAs_DiffRings(), denoptim.graph.DGraphTest.testSameAs_DiffSymmSet(), denoptim.graph.DGraphTest.testSameAs_DiffVertex(), denoptim.graph.DGraphTest.testSameAs_DisorderRings(), denoptim.graph.DGraphTest.testSameAs_Equal(), denoptim.graph.DGraphTest.testSameAs_SameRings(), denoptim.graph.DGraphTest.testSameAs_SameSymmSet(), and denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

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◆ sameAsRings()

boolean denoptim.graph.DGraph.sameAsRings	(	StringBuilder	reason,
		Map< Vertex, Vertex >	vertexMap,
		Ring	rT,
		Vertex	vhT,
		Vertex	vtT,
		Ring	rO
	)

private

Definition at line 3775 of file DGraph.java.

References denoptim.graph.Ring.getHeadVertex(), denoptim.graph.Ring.getSize(), denoptim.graph.Ring.getTailVertex(), and denoptim.graph.Ring.getVertexAtPosition().

Referenced by denoptim.graph.DGraph.sameAs().

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◆ setCandidateClosableChains()

void denoptim.graph.DGraph.setCandidateClosableChains ( ArrayList< ClosableChain > closableChains )

Definition at line 705 of file DGraph.java.

References denoptim.graph.DGraph.closableChains.

Referenced by denoptim.ga.EAUtils.buildGraph(), and denoptim.graph.DGraph.clone().

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◆ setCandidateOwner()

void denoptim.graph.DGraph.setCandidateOwner ( Candidate candidate )

Sets the reference to the candidate item that is defined by this graph.

Parameters

candidate the candidate owner.

Definition at line 239 of file DGraph.java.

References denoptim.graph.DGraph.candidate.

Referenced by denoptim.graph.Candidate.Candidate().

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◆ setEdgeList()

void denoptim.graph.DGraph.setEdgeList ( ArrayList< Edge > edges )

Definition at line 687 of file DGraph.java.

References denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

◆ setGraphId()

void denoptim.graph.DGraph.setGraphId ( int id )

Definition at line 258 of file DGraph.java.

References denoptim.graph.DGraph.graphId.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.buildGraph(), denoptim.graph.DGraph.clone(), denoptim.utils.GraphConversionTool.getGraphFromString(), denoptim.ga.GraphOperationsTest.getPairOfTestGraphs(), denoptim.ga.PopulationTest.getPairOfTestGraphsB(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxo(), denoptim.ga.PopulationTest.getPairOfTestGraphsBxoxo(), denoptim.combinatorial.GraphBuildingTask.GraphBuildingTask(), denoptim.gui.GUIGraphHandler.initializeCurrentGraph(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ setLocalMsg()

void denoptim.graph.DGraph.setLocalMsg ( String msg )

Definition at line 272 of file DGraph.java.

References denoptim.graph.DGraph.localMsg.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.buildGraph(), denoptim.graph.DGraph.clone(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringB(), denoptim.ga.GraphOperations.performMutation(), denoptim.ga.EAUtils.readCandidateFromFile(), and denoptim.combinatorial.CombinatorialExplorerByLayer.startNewGraphFromScaffold().

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◆ setRings()

void denoptim.graph.DGraph.setRings ( ArrayList< Ring > rings )

Definition at line 696 of file DGraph.java.

References denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

Referenced by denoptim.graph.DGraph.clone(), and denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets().

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◆ setScaffold()

static void denoptim.graph.DGraph.setScaffold ( Vertex v )

static

Update the graph so that the vertex argument is at the scaffold level i.e.

is the source of this graph. The vertex list of this graph will also be reordered in a way that corresponds to the BFS.

Parameters

v	vertex to set as scaffold

Definition at line 6863 of file DGraph.java.

References denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.AttachmentPoint.getEdgeUser(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.AttachmentPoint.getOwner(), denoptim.graph.Vertex.getVertexId(), and denoptim.graph.DGraph.setVertexList().

Referenced by denoptim.ga.GraphOperationsTest.getFusedRings(), and denoptim.graph.DGraph.reorderVertexList().

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◆ setSymmetricVertexSets()

void denoptim.graph.DGraph.setSymmetricVertexSets ( List< SymmetricVertexes > symVertices )

Definition at line 647 of file DGraph.java.

References denoptim.graph.DGraph.symVertices.

Referenced by denoptim.graph.DGraph.clone().

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◆ setTemplateJacket()

void denoptim.graph.DGraph.setTemplateJacket ( Template template )

Sets the reference to a template that embeds this graph, i.e., this graph's "jacket" template.

Parameters

denoptimTemplate the jacket template

Definition at line 6922 of file DGraph.java.

Referenced by denoptim.graph.Template.setInnerGraph().

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◆ setVertexList()

void denoptim.graph.DGraph.setVertexList ( ArrayList< Vertex > vertices )

Definition at line 678 of file DGraph.java.

References denoptim.graph.DGraph.gVertices, denoptim.graph.DGraph.jGraph, and denoptim.graph.DGraph.jGraphKernel.

Referenced by denoptim.graph.DGraph.setScaffold().

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◆ storeCurrentVertexIDs()

void denoptim.graph.DGraph.storeCurrentVertexIDs ( )

Copies the current vertexID of each vertex into a property of the vertex itself.

Use this to keep a memory of the vertex IDs in any given moment.

Definition at line 6982 of file DGraph.java.

References denoptim.graph.DGraph.gVertices, and denoptim.constants.DENOPTIMConstants.STOREDVID.

◆ toJson()

String denoptim.graph.DGraph.toJson ( )

Produces a string that represents this graph and that adheres to the JSON format.

Returns: the JSON format as a single string

Definition at line 6660 of file DGraph.java.

References denoptim.json.DENOPTIMgson.getWriter().

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.DGraphTest.testFromToJSON(), and denoptim.io.DenoptimIOTest.testSerializeDeserializeDENOPTIMGraphs().

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◆ toString()

String denoptim.graph.DGraph.toString ( )

Definition at line 2680 of file DGraph.java.

References denoptim.graph.DGraph.gEdges, denoptim.graph.DGraph.graphId, denoptim.graph.DGraph.gRings, denoptim.graph.DGraph.gVertices, and denoptim.graph.DGraph.symVertices.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.graph.DGraph.checkConsistency(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.programs.genetweeker.GeneOpsRunner.runMutation(), and denoptim.programs.graphlisthandler.GraphListsHandler.runProgram().

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Member Data Documentation

◆ apCounter

AtomicInteger denoptim.graph.DGraph.apCounter = new AtomicInteger(1)

private

Generator of unique AP identifiers within this graph.

Definition at line 171 of file DGraph.java.

Referenced by denoptim.graph.DGraph.ensureUniqueApIDs(), and denoptim.graph.DGraph.getUniqueAPIndex().

◆ candidate

Candidate denoptim.graph.DGraph.candidate

package

Reference to the candidate entity owning this graph, or null.

Definition at line 144 of file DGraph.java.

Referenced by denoptim.graph.DGraph.getCandidateOwner(), and denoptim.graph.DGraph.setCandidateOwner().

◆ closableChains

List<ClosableChain> denoptim.graph.DGraph.closableChains

package

The potentially closable chains of vertices.

Definition at line 121 of file DGraph.java.

Referenced by denoptim.graph.DGraph.cleanup(), denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.DGraph(), denoptim.graph.DGraph.getClosableChains(), denoptim.graph.DGraph.setCandidateClosableChains(), and denoptim.graph.DGraphTest.testClone().

◆ gEdges

List<Edge> denoptim.graph.DGraph.gEdges

package

The edges belonging to this graph.

Definition at line 111 of file DGraph.java.

◆ graphId

int denoptim.graph.DGraph.graphId

package

Definition at line 126 of file DGraph.java.

Referenced by denoptim.graph.DGraph.clone(), denoptim.graph.Candidate.compareTo(), denoptim.graph.DGraph.getGraphId(), denoptim.graph.DGraph.DENOPTIMGraphSerializer.serialize(), denoptim.graph.DGraph.setGraphId(), denoptim.graph.DGraphTest.testClone(), and denoptim.graph.DGraph.toString().

◆ gRings

List<Ring> denoptim.graph.DGraph.gRings

package

The rings defined in this graph.

Definition at line 116 of file DGraph.java.

◆ gVertices

List<Vertex> denoptim.graph.DGraph.gVertices

package

The vertices belonging to this graph.

Definition at line 106 of file DGraph.java.

◆ jGraph

DefaultUndirectedGraph<Vertex, UndirectedEdge> denoptim.graph.DGraph.jGraph = null

private

JGraph representation used to detect DENOPTIM-isomorphism.

Definition at line 155 of file DGraph.java.

◆ jGraphKernel

DefaultUndirectedGraph<Node, NodeConnection> denoptim.graph.DGraph.jGraphKernel = null

private

JGraph representation used to detect DENOPTIM-isostructural graphs.

Definition at line 161 of file DGraph.java.

◆ localMsg

String denoptim.graph.DGraph.localMsg

package

A free-format string used to record simple properties in the graph.

For instance, whether this graph comes from a given initial population or is generated anew from scratch, or from mutation/crossover.

Definition at line 139 of file DGraph.java.

Referenced by denoptim.graph.DGraph.clone(), denoptim.graph.DGraph.DGraph(), denoptim.graph.DGraph.getLocalMsg(), denoptim.graph.DGraph.setLocalMsg(), and denoptim.graph.DGraphTest.testClone().

◆ symVertices

List<SymmetricVertexes> denoptim.graph.DGraph.symVertices

private

Definition at line 132 of file DGraph.java.

◆ templateJacket

Template denoptim.graph.DGraph.templateJacket

package

Reference to the Template embedding this graph.

Definition at line 149 of file DGraph.java.

Referenced by denoptim.graph.Template.addInnerToOuterAPMapping(), denoptim.graph.AttachmentPoint.getEdgeUserThroughout(), denoptim.graph.DGraph.getEmbeddingPath(), denoptim.graph.DGraph.getOutermostGraphOwner(), denoptim.graph.DGraph.getTemplateJacket(), denoptim.graph.DGraph.insertSingleVertex(), denoptim.graph.AttachmentPoint.isAvailableThroughout(), denoptim.graph.DGraph.removeChainUpToBranching(), denoptim.graph.Template.removeProjectionOfInnerAP(), denoptim.graph.DGraph.removeSingleVertexAndWeld(), and denoptim.graph.DGraph.replaceSingleSubGraph().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/graph/DGraph.java

graphY	where we want to find the analogous of `graphA`.
graphB	the graph `graphB` where `path` points to `graphA`.
path	the embedding path of `graphA` in `graphB`.

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Package Functions

Package Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DGraph() [1/5]

◆ DGraph() [2/5]

◆ DGraph() [3/5]

◆ DGraph() [4/5]

◆ DGraph() [5/5]

Member Function Documentation

◆ addCappingGroups() [1/2]

◆ addCappingGroups() [2/2]

◆ addEdge()

◆ addRing() [1/3]

◆ addRing() [2/3]

◆ addRing() [3/3]

◆ addSymmetricSetOfVertices()

◆ addVertex()

◆ appendGraphOnAP() [1/2]

◆ appendGraphOnAP() [2/2]

◆ appendGraphOnGraph() [1/2]

◆ appendGraphOnGraph() [2/2]

◆ appendVertexOnAP()

◆ areApsUsedBySymmetricUsers()

◆ changeSignOfVertexID()

◆ checkConsistency() [1/2]

◆ checkConsistency() [2/2]

◆ cleanup()

◆ clone()

◆ compareGraphNodes() [1/2]

◆ compareGraphNodes() [2/2]

◆ containsAtoms()

◆ containsOrEmbedsVertex()

◆ containsVertex()

◆ containsVertexID()

◆ convertSymmetricLabelsToSymmetricSets()

◆ detectSymVertexSets()

◆ directedPathExists()

◆ editGraph()

◆ embedPatternsInTemplates() [1/2]

◆ embedPatternsInTemplates() [2/2]

◆ ensureUniqueApIDs()

◆ extractPattern() [1/2]

◆ extractPattern() [2/2]

◆ extractSubgraph() [1/7]

◆ extractSubgraph() [2/7]

◆ extractSubgraph() [3/7]

◆ extractSubgraph() [4/7]

◆ extractSubgraph() [5/7]

◆ extractSubgraph() [6/7]

◆ extractSubgraph() [7/7]

◆ findSymmetrySetsOfChildVertexes()

◆ findVertices() [1/2]

◆ findVertices() [2/2]

◆ findVerticesIds()

◆ fixEdgeDirections() [1/2]

◆ fixEdgeDirections() [2/2]

◆ fromJson() [1/2]

◆ fromJson() [2/2]

◆ getAPOnLeftVertexID()

◆ getAPWithId()

◆ getAttachmentPoints()

◆ getAvailableAPs()

◆ getAvailableAPsThroughout()

◆ getBondingAPIndex()

◆ getBranchIdOfVertex()

◆ getBranchIdOfVertexAsStr()

◆ getBranchIdOfVertexAtPosition()

◆ getCandidateOwner()

◆ getChildrenTree() [1/4]

◆ getChildrenTree() [2/4]

◆ getChildrenTree() [3/4]

◆ getChildrenTree() [4/4]